Every once in a while, when I log off and relog, sometimes blocks respawn in places I have already mined out(Sometimes also trapping me in said blocks), and if there are any other blocks there(i.e. Chests, Redstone components, etc, they will be overwritten as blocks of stone, dirt, ore, etc(You lose the items completely)
Edit: Upon flying around in ./gamemode 3(spectator mode) I found the blocks that were overwritten by the stone, dirt, etc. moved to a different part of the map nearby.
Edit 2: I have included photos of my wheat farm that dissappeared, and find below in comments the requested game log.
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After having this issue:
Please attach the complete output of the "Game Output (Your Minecraft name) " which can be found on the fourth tab of the launcher to this ticket.
If the launcher closes after game start, please edit your profile and select "Launcher visibility" then, "Keep the launcher open".

This happens rarely, however it seems that terrain also keeps changing after I log off and relog.

Completely ignored arguments: [--nativeLauncherVersion, 286]
[09:03:25] [Client thread/INFO]: Setting user: QuestionTues_FTW
[09:03:25] [Client thread/INFO]: (Session ID is token:47a862c3f6534b6faf2a12856a741014:5a11c5427af44e118e3f0c9db49cda19)
[09:03:28] [Client thread/INFO]: LWJGL Version: 2.9.4
[09:03:29] [Client thread/INFO]: Reloading ResourceManager: Default
[09:03:31] [Sound Library Loader/INFO]: Starting up SoundSystem...
[09:03:31] [Thread-6/INFO]: Initializing LWJGL OpenAL
[09:03:31] [Thread-6/INFO]: (The LWJGL binding of OpenAL. For more information, see http://www.lwjgl.org)
[09:03:33] [Thread-6/INFO]: OpenAL initialized.
[09:03:33] [Sound Library Loader/INFO]: Sound engine started
[09:03:49] [Client thread/INFO]: Created: 512x512 textures-atlas
[09:05:11] [Client thread/ERROR]: Exception reading C:\Users\Ian\AppData\Roaming\.minecraft\saves\damn it\level.dat
java.util.zip.ZipException: Not in GZIP format
at java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:165) ~[?:1.8.0_25]
at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:79) ~[?:1.8.0_25]
at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:91) ~[?:1.8.0_25]
at dx.a(SourceFile:13) ~[1.8.8.jar:?]
at atn.c(SourceFile:62) [1.8.8.jar:?]
at atk.b(SourceFile:52) [1.8.8.jar:?]
at axv.f(SourceFile:87) [1.8.8.jar:?]
at axv.b(SourceFile:59) [1.8.8.jar:?]
at axu.a(SourceFile:376) [1.8.8.jar:?]
at ave.a(SourceFile:819) [1.8.8.jar:?]
at aya.a(SourceFile:215) [1.8.8.jar:?]
at axu.a(SourceFile:350) [1.8.8.jar:?]
at aya.a(SourceFile:468) [1.8.8.jar:?]
at axu.k(SourceFile:413) [1.8.8.jar:?]
at axu.p(SourceFile:390) [1.8.8.jar:?]
at ave.s(SourceFile:1498) [1.8.8.jar:?]
at ave.av(SourceFile:889) [1.8.8.jar:?]
at ave.a(SourceFile:325) [1.8.8.jar:?]
at net.minecraft.client.main.Main.main(SourceFile:124) [1.8.8.jar:?]
[09:05:13] [Server thread/INFO]: Starting integrated minecraft server version 1.8.8
[09:05:13] [Server thread/INFO]: Generating keypair
java.util.zip.ZipException: Not in GZIP format
at java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:165)
at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:79)
at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:91)
at dx.a(SourceFile:13)
at aua.a(SourceFile:43)
at le.b(SourceFile:127)
at bpo.a(SourceFile:96)
at bpo.i(SourceFile:128)
at net.minecraft.server.MinecraftServer.run(SourceFile:421)
at java.lang.Thread.run(Thread.java:745)
java.util.zip.ZipException: Not in GZIP format
at java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:165)
at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:79)
at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:91)
at dx.a(SourceFile:13)
at aua.a(SourceFile:43)
at kz.b(SourceFile:70)
at bpo.a(SourceFile:100)
at bpo.i(SourceFile:128)
at net.minecraft.server.MinecraftServer.run(SourceFile:421)
at java.lang.Thread.run(Thread.java:745)
java.util.zip.ZipException: Not in GZIP format
at java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:165)
at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:79)
at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:91)
at dx.a(SourceFile:13)
at aua.a(SourceFile:43)
at kz.b(SourceFile:70)
at bpo.a(SourceFile:100)
at bpo.i(SourceFile:128)
at net.minecraft.server.MinecraftServer.run(SourceFile:421)
at java.lang.Thread.run(Thread.java:745)
[09:05:13] [Server thread/INFO]: Preparing start region for level 0
[09:05:14] [Server thread/INFO]: Preparing spawn area: 32%
[09:05:15] [Server thread/INFO]: Changing view distance to 12, from 10
[09:05:16] [Server thread/INFO]: QuestionTues_FTW[local:E:cdf989e6] logged in with entity id 254 at (805.755717162518, 48.0, -92.69999998807906)
[09:05:16] [Server thread/INFO]: QuestionTues_FTW joined the game
[09:05:17] [Server thread/ERROR]: Chunk file at 49,-3 is in the wrong location; relocating. (Expected 49, -3, got 50, -4)
[09:05:17] [Server thread/ERROR]: Chunk file at 50,-11 is in the wrong location; relocating. (Expected 50, -11, got 51, -2)
[09:05:18] [Server thread/WARN]: Wrong location! (51, -2) should be (50, -11), we['Zombie'/385, l='More Fish', x=825.50, y=13.00, z=-29.50]
[09:05:18] [Server thread/ERROR]: Chunk file at 50,-4 is in the wrong location; relocating. (Expected 50, -4, got 54, -10)
[09:05:18] [Server thread/WARN]: Wrong location! (54, -10) should be (50, -4), we['Zombie'/396, l='More Fish', x=875.50, y=38.00, z=-147.50]
[09:05:18] [Server thread/WARN]: Wrong location! (54, -10) should be (50, -4), we['Zombie'/397, l='More Fish', x=874.75, y=38.00, z=-144.71]
[09:05:18] [Server thread/ERROR]: Chunk file at 51,-2 is in the wrong location; relocating. (Expected 51, -2, got 50, -3)
[09:05:18] [Server thread/ERROR]: Chunk file at 54,-11 is in the wrong location; relocating. (Expected 54, -11, got 49, -3)
[09:05:18] [Server thread/WARN]: Wrong location! (49, -3) should be (54, -11), we['Zombie'/473, l='More Fish', x=788.50, y=27.00, z=-44.50]
[09:05:18] [Server thread/WARN]: Wrong location! (49, -3) should be (54, -11), tv['Sheep'/474, l='More Fish', x=799.02, y=67.00, z=-34.95]
[09:05:18] [Server thread/WARN]: Wrong location! (49, -3) should be (54, -11), tn['Chicken'/475, l='More Fish', x=790.36, y=65.00, z=-46.58]
[09:05:18] [Server thread/WARN]: Wrong location! (49, -3) should be (54, -11), uz['item.item.egg'/476, l='More Fish', x=790.53, y=65.00, z=-46.17]
[09:05:18] [Server thread/ERROR]: Chunk file at 54,-10 is in the wrong location; relocating. (Expected 54, -10, got 55, -5)
[09:05:18] [Server thread/WARN]: Wrong location! (55, -5) should be (54, -10), vo['Enderman'/478, l='More Fish', x=895.50, y=20.00, z=-66.50]
[09:05:18] [Server thread/ERROR]: Chunk file at 54,-6 is in the wrong location; relocating. (Expected 54, -6, got 56, -10)
[09:05:18] [Server thread/WARN]: Wrong location! (56, -10) should be (54, -6), vn['Creeper'/489, l='More Fish', x=907.50, y=30.00, z=-148.50]
[09:05:18] [Server thread/WARN]: Wrong location! (56, -10) should be (54, -6), vn['Creeper'/490, l='More Fish', x=906.50, y=30.00, z=-149.50]
[09:05:18] [Server thread/WARN]: Wrong location! (56, -10) should be (54, -6), vn['Creeper'/491, l='More Fish', x=906.50, y=30.00, z=-148.50]
[09:05:18] [Server thread/WARN]: Wrong location! (56, -10) should be (54, -6), vn['Creeper'/492, l='More Fish', x=911.50, y=30.00, z=-150.50]
[09:05:18] [Server thread/WARN]: Wrong location! (56, -10) should be (54, -6), tn['Chicken'/493, l='More Fish', x=899.33, y=62.67, z=-150.12]
[09:05:18] [Server thread/WARN]: Wrong location! (56, -10) should be (54, -6), tn['Chicken'/494, l='More Fish', x=903.54, y=62.59, z=-145.42]
[09:05:18] [Server thread/WARN]: Wrong location! (56, -10) should be (54, -6), uz['item.item.egg'/495, l='More Fish', x=903.21, y=61.00, z=-144.42]
[09:05:19] [Server thread/ERROR]: Chunk file at 56,-10 is in the wrong location; relocating. (Expected 56, -10, got 57, -10)
[09:05:19] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 3836ms behind, skipping 76 tick(s)
[09:05:20] [Server thread/INFO]: Saving and pausing game...
[09:05:20] [Server thread/INFO]: Saving chunks for level 'More Fish'/Overworld
[09:05:21] [Server thread/INFO]: Saving chunks for level 'More Fish'/Nether
[09:05:21] [Server thread/INFO]: Saving chunks for level 'More Fish'/The End
[09:05:52] [Server thread/INFO]: Saving and pausing game...
[09:05:52] [Server thread/INFO]: Saving chunks for level 'More Fish'/Overworld
[09:05:52] [Server thread/INFO]: Saving chunks for level 'More Fish'/Nether
[09:05:52] [Server thread/INFO]: Saving chunks for level 'More Fish'/The End
[09:06:12] [Server thread/INFO]: [QuestionTues_FTW: Set own game mode to Spectator Mode]
[09:06:12] [Client thread/INFO]: [CHAT] Your game mode has been updated
[09:06:28] [Server thread/INFO]: Saving and pausing game...
[09:06:28] [Server thread/INFO]: Saving chunks for level 'More Fish'/Overworld
[09:06:28] [Server thread/INFO]: Saving chunks for level 'More Fish'/Nether
[09:06:28] [Server thread/INFO]: Saving chunks for level 'More Fish'/The End
[09:07:29] [Server thread/INFO]: [QuestionTues_FTW: Set own game mode to Survival Mode]
[09:07:29] [Client thread/INFO]: [CHAT] Your game mode has been updated
[09:07:32] [Client thread/INFO]: [CHAT] Saved screenshot as 2015-09-22_09.07.32.png
[09:07:35] [Server thread/INFO]: Saving and pausing game...
[09:07:35] [Server thread/INFO]: Saving chunks for level 'More Fish'/Overworld
[09:07:35] [Server thread/INFO]: Saving chunks for level 'More Fish'/Nether
[09:07:35] [Server thread/INFO]: Saving chunks for level 'More Fish'/The End
[09:07:38] [Client thread/INFO]: [CHAT] Saved screenshot as 2015-09-22_09.07.38.png
[09:07:39] [Server thread/INFO]: Saving and pausing game...
[09:07:40] [Server thread/INFO]: Saving chunks for level 'More Fish'/Overworld
[09:07:40] [Server thread/INFO]: Saving chunks for level 'More Fish'/Nether
[09:07:40] [Server thread/INFO]: Saving chunks for level 'More Fish'/The End
java.io.IOException: Stream Closed
at java.io.RandomAccessFile.seek0(Native Method)
at java.io.RandomAccessFile.seek(RandomAccessFile.java:540)
at anh.a(SourceFile:315)
at anh.a(SourceFile:255)
at anh$a.close(SourceFile:236)
at java.util.zip.DeflaterOutputStream.close(DeflaterOutputStream.java:241)
at java.io.FilterOutputStream.close(FilterOutputStream.java:159)
at anj.b(SourceFile:140)
at anj.c(SourceFile:124)
at auc.c(SourceFile:37)
at auc.run(SourceFile:30)
at java.lang.Thread.run(Thread.java:745)
[09:07:40] [Server thread/INFO]: Stopping server
[09:07:40] [Server thread/INFO]: Saving players
[09:07:40] [Server thread/INFO]: Saving worlds
[09:07:40] [Server thread/INFO]: Saving chunks for level 'More Fish'/Overworld
[09:07:40] [Server thread/INFO]: Saving chunks for level 'More Fish'/Nether
[09:07:40] [Server thread/INFO]: Saving chunks for level 'More Fish'/The End
[09:08:06] [Client thread/INFO]: Stopping!
[09:08:06] [Client thread/INFO]: SoundSystem shutting down...
[09:08:06] [Client thread/WARN]: Author: Paul Lamb, www.paulscode.com
Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release

Broken world, see MC-87353

Your world is broken.
java.util.zip.ZipException: Not in GZIP format
[09:05:17] [Server thread/ERROR]: Chunk file at 49,-3 is in the wrong location; relocating. (Expected 49, -3, got 50, -4)
Duplicate of MC-87353