Every time a player joins and entities start to load, the console is spammed with entity error spam. This can be recreated simply by joining a world. Tested on a vanilla server with no plugins, etc. Not tested on Single player on a local world.
[05:40:22] [Server thread/INFO]: Starting minecraft server version 15w42a
[05:40:22] [Server thread/INFO]: Loading properties
[05:40:22] [Server thread/INFO]: Default game type: SURVIVAL
[05:40:22] [Server thread/INFO]: Generating keypair
[05:40:22] [Server thread/INFO]: Starting Minecraft server on *:25565
[05:40:23] [Server thread/INFO]: Using epoll channel type
[05:40:23] [Server thread/INFO]: Preparing level "G'hira"
[05:40:23] [Server thread/INFO]: Preparing start region for level 0
[05:40:24] [Server thread/INFO]: Preparing spawn area: 7%
[05:40:25] [Server thread/INFO]: Preparing spawn area: 59%
[05:40:26] [Server thread/INFO]: Done (3.250s)! For help, type "help" or "?"
[13:18:07] [User Authenticator #1/INFO]: UUID of player _Arkadious_ is e85941b2-1920-48ef-a294-94f8b3330dba
[13:18:07] [Server thread/INFO]: _Arkadious_[/71.65.57.231:61714] logged in with entity id 416 at (80.35313335204097, 74.0, -185.47141401396095)
[13:18:07] [Server thread/INFO]: _Arkadious_ joined the game
[13:18:07] [Server thread/WARN]: Tried to add entity Sheep with pending removal and duplicate UUID c9e59fee-3916-47c9-b170-cbfe6333b3c5
[13:18:07] [Server thread/WARN]: Tried to add entity Bat with pending removal and duplicate UUID 18fca41b-0cf6-480c-b095-a151e1f5cc12
[13:18:07] [Server thread/WARN]: Tried to add entity Bat with pending removal and duplicate UUID 2ddd1cef-138e-40b1-8901-1da175e419ea
[13:18:07] [Server thread/WARN]: Tried to add entity Spider with pending removal and duplicate UUID 6ec25578-c431-48aa-b9f2-98d04d4b90f4
[13:18:07] [Server thread/WARN]: Tried to add entity Zombie with pending removal and duplicate UUID 766f2ed8-2f20-4248-9f88-f5ed00172c7f
[13:18:07] [Server thread/WARN]: Tried to add entity Zombie with pending removal and duplicate UUID e7030f01-0094-4cd9-85d2-f90d292f294e
[13:18:07] [Server thread/WARN]: Tried to add entity Sheep with pending removal and duplicate UUID 6812c4fc-369e-41b5-bf6b-cc5f20454bb8
[13:18:07] [Server thread/WARN]: Tried to add entity Chicken with pending removal and duplicate UUID c6a199f0-3e67-4f4c-a7f5-5d2da37179bd
[13:18:07] [Server thread/WARN]: Tried to add entity Item with pending removal and duplicate UUID 94e2de15-2a59-44aa-ad1a-a2a43e828efe
[13:18:07] [Server thread/WARN]: Tried to add entity Bat with pending removal and duplicate UUID 61cb29b4-a2ec-4cf9-ae25-60456de34af4
[13:18:07] [Server thread/WARN]: Tried to add entity Bat with pending removal and duplicate UUID f40636d9-bf8c-49c6-ab2b-31c4b78991ad
[13:18:08] [Server thread/WARN]: Tried to add entity EntityHorse with pending removal and duplicate UUID a1ec85db-860a-43f2-913b-35c5b4c0eaed
[13:18:08] [Server thread/WARN]: Tried to add entity Creeper with pending removal and duplicate UUID 82f3c815-975e-41cd-aadd-7737e6341e9e
[13:18:08] [Server thread/WARN]: Tried to add entity Pig with pending removal and duplicate UUID 5ae38a31-03bf-4aa2-a8fe-c4913ac8513a
[13:18:08] [Server thread/WARN]: Tried to add entity Pig with pending removal and duplicate UUID ffaf3d9a-c17e-4501-9174-36c498759234
[13:18:08] [Server thread/WARN]: Tried to add entity Creeper with pending removal and duplicate UUID eaf9a528-d226-4012-b5ec-d45532dac3be
[13:18:08] [Server thread/WARN]: Tried to add entity EntityHorse with pending removal and duplicate UUID 7510b580-3005-4a87-b53c-13fdebe0c224
[13:18:08] [Server thread/WARN]: Tried to add entity Pig with pending removal and duplicate UUID c1fa0fb4-8f19-4e51-a6a3-0117e79a9a94
[13:18:08] [Server thread/WARN]: Tried to add entity Creeper with pending removal and duplicate UUID c8e2e848-f4c7-4774-9249-516c26e15184
[13:18:08] [Server thread/WARN]: Tried to add entity Skeleton with pending removal and duplicate UUID d51027cd-08f5-4ecd-8f97-b96cbf95794c
[13:36:35] [Server thread/WARN]: Tried to add entity Bat with pending removal and duplicate UUID 0ec771c9-f8ab-4f9c-b87f-a2e3597df6bf
[13:36:35] [Server thread/WARN]: Tried to add entity ItemFrame with pending removal and duplicate UUID fcaeb4ab-8a27-43e5-a98b-fa232fe2d40e
[13:36:35] [Server thread/WARN]: Tried to add entity ItemFrame with pending removal and duplicate UUID 4ef9da7d-5b58-4fb2-bfe3-ae582d859e12
[13:36:35] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID 0cb942f6-b7af-4ede-85cf-e5379eea79ca
[13:36:35] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID 4b0642ef-b780-4675-9a97-1cabebb3df8d
[13:36:35] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID f1336938-8522-49f4-8ef0-3f6f411e1b03
[13:36:35] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID fca44f7e-0a03-493f-9a59-f1b54b15855b
[13:36:41] [Server thread/WARN]: Tried to add entity Bat with pending removal and duplicate UUID 0ec771c9-f8ab-4f9c-b87f-a2e3597df6bf
[13:36:41] [Server thread/WARN]: Tried to add entity ItemFrame with pending removal and duplicate UUID fcaeb4ab-8a27-43e5-a98b-fa232fe2d40e
[13:36:41] [Server thread/WARN]: Tried to add entity ItemFrame with pending removal and duplicate UUID 4ef9da7d-5b58-4fb2-bfe3-ae582d859e12
[13:36:41] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID 0cb942f6-b7af-4ede-85cf-e5379eea79ca
[13:36:41] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID 4b0642ef-b780-4675-9a97-1cabebb3df8d
[13:36:41] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID f1336938-8522-49f4-8ef0-3f6f411e1b03
[13:36:41] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID fca44f7e-0a03-493f-9a59-f1b54b15855b
[13:37:13] [Server thread/WARN]: Tried to add entity Bat with pending removal and duplicate UUID e51241cb-c77f-43a3-92cb-3aefaf560f05
[13:39:18] [Server thread/WARN]: Tried to add entity Bat with pending removal and duplicate UUID 0ec771c9-f8ab-4f9c-b87f-a2e3597df6bf
[13:39:18] [Server thread/WARN]: Tried to add entity ItemFrame with pending removal and duplicate UUID fcaeb4ab-8a27-43e5-a98b-fa232fe2d40e
[13:39:18] [Server thread/WARN]: Tried to add entity ItemFrame with pending removal and duplicate UUID 4ef9da7d-5b58-4fb2-bfe3-ae582d859e12
[13:39:18] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID 0cb942f6-b7af-4ede-85cf-e5379eea79ca
[13:39:18] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID 4b0642ef-b780-4675-9a97-1cabebb3df8d
[13:39:18] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID f1336938-8522-49f4-8ef0-3f6f411e1b03
[13:39:18] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID fca44f7e-0a03-493f-9a59-f1b54b15855b
[13:39:41] [Server thread/WARN]: Tried to add entity Bat with pending removal and duplicate UUID 0ec771c9-f8ab-4f9c-b87f-a2e3597df6bf
[13:39:41] [Server thread/WARN]: Tried to add entity ItemFrame with pending removal and duplicate UUID fcaeb4ab-8a27-43e5-a98b-fa232fe2d40e
[13:39:41] [Server thread/WARN]: Tried to add entity ItemFrame with pending removal and duplicate UUID 4ef9da7d-5b58-4fb2-bfe3-ae582d859e12
[13:39:41] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID 0cb942f6-b7af-4ede-85cf-e5379eea79ca
[13:39:41] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID 4b0642ef-b780-4675-9a97-1cabebb3df8d
[13:39:41] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID f1336938-8522-49f4-8ef0-3f6f411e1b03
[13:39:41] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID fca44f7e-0a03-493f-9a59-f1b54b15855b
[13:42:41] [Server thread/WARN]: Tried to add entity Skeleton with pending removal and duplicate UUID 0d377940-850e-476a-9e42-2616e64cea96
[13:42:41] [Server thread/WARN]: Tried to add entity Spider with pending removal and duplicate UUID bf2fb948-e689-4879-93ff-367c5009d19c
[13:49:42] [Server thread/WARN]: Tried to add entity Bat with pending removal and duplicate UUID 0ec771c9-f8ab-4f9c-b87f-a2e3597df6bf
[13:49:42] [Server thread/WARN]: Tried to add entity ItemFrame with pending removal and duplicate UUID fcaeb4ab-8a27-43e5-a98b-fa232fe2d40e
[13:49:42] [Server thread/WARN]: Tried to add entity ItemFrame with pending removal and duplicate UUID 4ef9da7d-5b58-4fb2-bfe3-ae582d859e12
[13:49:42] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID 0cb942f6-b7af-4ede-85cf-e5379eea79ca
[13:49:42] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID 4b0642ef-b780-4675-9a97-1cabebb3df8d
[13:49:42] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID f1336938-8522-49f4-8ef0-3f6f411e1b03
[13:49:42] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID fca44f7e-0a03-493f-9a59-f1b54b15855b
[13:50:11] [Server thread/WARN]: Tried to add entity Bat with pending removal and duplicate UUID 0ec771c9-f8ab-4f9c-b87f-a2e3597df6bf
[13:50:11] [Server thread/WARN]: Tried to add entity ItemFrame with pending removal and duplicate UUID fcaeb4ab-8a27-43e5-a98b-fa232fe2d40e
[13:50:11] [Server thread/WARN]: Tried to add entity ItemFrame with pending removal and duplicate UUID 4ef9da7d-5b58-4fb2-bfe3-ae582d859e12
[13:50:11] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID 0cb942f6-b7af-4ede-85cf-e5379eea79ca
[13:50:11] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID 4b0642ef-b780-4675-9a97-1cabebb3df8d
[13:50:11] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID f1336938-8522-49f4-8ef0-3f6f411e1b03
[13:50:11] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID fca44f7e-0a03-493f-9a59-f1b54b15855b
[14:00:04] [Server thread/WARN]: Tried to add entity Bat with pending removal and duplicate UUID 0ec771c9-f8ab-4f9c-b87f-a2e3597df6bf
[14:00:04] [Server thread/WARN]: Tried to add entity ItemFrame with pending removal and duplicate UUID fcaeb4ab-8a27-43e5-a98b-fa232fe2d40e
[14:00:04] [Server thread/WARN]: Tried to add entity ItemFrame with pending removal and duplicate UUID 4ef9da7d-5b58-4fb2-bfe3-ae582d859e12
[14:00:04] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID 0cb942f6-b7af-4ede-85cf-e5379eea79ca
[14:00:04] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID 4b0642ef-b780-4675-9a97-1cabebb3df8d
[14:00:04] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID f1336938-8522-49f4-8ef0-3f6f411e1b03
[14:00:04] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID fca44f7e-0a03-493f-9a59-f1b54b15855b
[14:10:30] [Server thread/WARN]: Tried to add entity Bat with pending removal and duplicate UUID 0ec771c9-f8ab-4f9c-b87f-a2e3597df6bf
[14:10:30] [Server thread/WARN]: Tried to add entity ItemFrame with pending removal and duplicate UUID fcaeb4ab-8a27-43e5-a98b-fa232fe2d40e
[14:10:30] [Server thread/WARN]: Tried to add entity ItemFrame with pending removal and duplicate UUID 4ef9da7d-5b58-4fb2-bfe3-ae582d859e12
[14:10:30] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID 0cb942f6-b7af-4ede-85cf-e5379eea79ca
[14:10:30] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID 4b0642ef-b780-4675-9a97-1cabebb3df8d
[14:10:30] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID f1336938-8522-49f4-8ef0-3f6f411e1b03
[14:10:30] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID fca44f7e-0a03-493f-9a59-f1b54b15855b
[14:11:11] [Server thread/WARN]: Tried to add entity Bat with pending removal and duplicate UUID 0ec771c9-f8ab-4f9c-b87f-a2e3597df6bf
[14:11:11] [Server thread/WARN]: Tried to add entity ItemFrame with pending removal and duplicate UUID fcaeb4ab-8a27-43e5-a98b-fa232fe2d40e
[14:11:11] [Server thread/WARN]: Tried to add entity ItemFrame with pending removal and duplicate UUID 4ef9da7d-5b58-4fb2-bfe3-ae582d859e12
[14:11:11] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID 0cb942f6-b7af-4ede-85cf-e5379eea79ca
[14:11:11] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID 4b0642ef-b780-4675-9a97-1cabebb3df8d
[14:11:11] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID f1336938-8522-49f4-8ef0-3f6f411e1b03
[14:11:11] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID fca44f7e-0a03-493f-9a59-f1b54b15855b
[14:13:26] [Server thread/WARN]: Tried to add entity Zombie with pending removal and duplicate UUID df8d4392-3f7d-437b-8411-f210bbd0acd9
[14:13:26] [Server thread/WARN]: Tried to add entity Zombie with pending removal and duplicate UUID 83735c73-96e5-405d-83ce-d60c3bad7d03
[14:13:26] [Server thread/WARN]: Tried to add entity Zombie with pending removal and duplicate UUID 74edca1c-16f8-48cc-ad23-3cc59f6b700d
[14:26:11] [Server thread/WARN]: Tried to add entity Bat with pending removal and duplicate UUID 2c900830-f369-4b21-845d-5fa2e4d91fb6
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Happy New Year Everyone!
This issue appears to be marked as resolved and waiting verification, however on my server this warning started appearing only after upgrading from to 1.8.8 Spigot and CraftBukit 1.8.8 from 1.8 on both. The majority I'm seeing today is "EntityHorse" that already exists with UUID 3c7c1b5d-7955-4901-b781-459b6882bcea. Occurs about every 44 ms intervals. An odd number to repeat on, but there does appear to be some kind of a pattern. I see 10 ms intervals as well. I do have portals, but no one has tried to put any animal/entity thru one. Would like to know if where in the code this is coming from. It has to be in one or both the upgraded server code.
Thanks!
Steve

@@unknown This bug tracker is for vanilla. You should contact Spigot/CraftBukkit developers instead.

That would make sense to contact Spigot/CraftBukkit if the issue was NOT in the vanilla (base Minecraft). Because it can be reproduced without any plugins, that says it is in the base product, not a plugin. This has been true for all my 30+ years in the software industry as an engineer, qa manager and systems administrator/dba.
Could a plugin be causing additional warnings? Sure - but if it is fixed in the base product, it stands to reason with a 99% probability it will be fixed for all.
Steve

@@unknown This error literally does not exist in the vanilla game's decompiled source for 1.8. This error was introduced in vanilla during the 1.9 snapshots. Your error literally cannot occur in 1.8 vanilla. If you remove plugins but keep Spigot/CraftBukkit, then you are still not in vanilla. You are using Spigot/CraftBukkit. They modify the game heavily. This bug tracker is not for any modded version of Minecraft in any manner.

Thanks Skylinerw - I was simply going by the reported issue "Every time a player joins and entities start to load, the console is spammed with entity error spam. This can be recreated simply by joining a world. Tested on a vanilla server with no plugins, etc. Not tested on Single player on a local world. " Plus the fact that this wasn't occurring in 1.8 and only started with 1.8.8 spigot and craftbukkit. I see your point though that they are basically taking the code and manipulating the "base/vanilla code" and adding their own. I'll reach out to them and see if they have ideas on what is causing it in their latest release.