Oftentimes the server can get spammed with warnings along the lines of:
[11:54:24] [Server thread/WARN]: Tried to add entity Sheep with pending removal and duplicate UUID d361162c-e5ef-41e8-8df9-741688e73c1a
[11:54:24] [Server thread/WARN]: Tried to add entity Villager with pending removal and duplicate UUID 44a5ac63-1215-4667-bed3-bdcde0055696
It appears that the root cause of these warnings is a delay of a tick (or maybe more) between entity removal, during which time a required chunk may be reloaded.
I have reproduced this in 14w49b Vanilla by flying around in creative at normal speed, but for a faster reproduction, the following may be helpful:
/give @p minecraft:golden_boots 1 0 {AttributeModifiers:[{AttributeName:"generic.movementSpeed",Name:"generic.movementSpeed",Amount:10,Operation:1,UUIDLeast:894654,UUIDMost:2872}],display:{Name:"Speed Boots",Lore:["Put on for a 10x Speed boost!"]}}
.
It is likely this issue also affects 1.8.8 but is simply unnoticed as the warnings have only been added in the current snapshot series.
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but I have not yet reproduced this behaviour in Vanilla.
Then it appears this ticket is... well, you know the word.

No,
The issue mentioned in this ticket has been reproduced in Vanilla 15w49b.
The corollary mentioned in the comment has not.
Can confirm in 15w50a.

and WAI per Searge's comment on MC-88922:
These log messages are "just" warnings that a potential problem with duplicate UUIDs was detected and prevented. It's not a problem, the code I wrote to fix the associated bug should work. I just left the messages in for now, so that I can see how often my code actually prevents it from happening, this will be changed eventually.
TL;DR: it's not a bug, just some useful debug logging
As a slightly related addendum, it appears that sometimes these duplicate entities can be saved across several chunks, but I have not yet reproduced this behaviour in Vanilla.