Chunks not saving

I was playing around with my server when I noticed that whenever I placed a block and whatnot it would not be there later. The server console is also littered with this error again and again.

11:19:16] [File IO Thread/ERROR]: Failed to save chunk
java.lang.IndexOutOfBoundsException: Index: 1544, Size: 1378
at java.util.ArrayList.rangeCheck(ArrayList.java:653) ~[?:1.8.0_25]
at java.util.ArrayList.set(ArrayList.java:444) ~[?:1.8.0_25]
at net.minecraft.world.chunk.storage.RegionFile.func_76706_a(RegionFile.java:226) ~[ath.class:?]
at net.minecraft.world.chunk.storage.RegionFile$ChunkBuffer.close(RegionFile.java:356) ~[ath$a.class:?]
at java.util.zip.DeflaterOutputStream.close(DeflaterOutputStream.java:241) ~[?:1.8.0_25]
at java.io.FilterOutputStream.close(FilterOutputStream.java:159) ~[?:1.8.0_25]
at java.io.FilterOutputStream.close(FilterOutputStream.java:159) ~[?:1.8.0_25]
at net.minecraft.world.chunk.storage.AnvilChunkLoader.func_183013_b(AnvilChunkLoader.java:243) ~[atj.class:?]
at net.minecraft.world.chunk.storage.AnvilChunkLoader.func_75814_c(AnvilChunkLoader.java:220) [atj.class:?]
at net.minecraft.world.storage.ThreadedFileIOBase.func_75736_b(SourceFile:37) [bbu.class:?]
at net.minecraft.world.storage.ThreadedFileIOBase.run(SourceFile:30) [bbu.class:?]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_25]
[11:19:37] [File IO Thread/ERROR]: Failed to save chunk
java.lang.IndexOutOfBoundsException: Index: 1560, Size: 1378
at java.util.ArrayList.rangeCheck(ArrayList.java:653) ~[?:1.8.0_25]
at java.util.ArrayList.set(ArrayList.java:444) ~[?:1.8.0_25]
at net.minecraft.world.chunk.storage.RegionFile.func_76706_a(RegionFile.java:226) ~[ath.class:?]
at net.minecraft.world.chunk.storage.RegionFile$ChunkBuffer.close(RegionFile.java:356) ~[ath$a.class:?]
at java.util.zip.DeflaterOutputStream.close(DeflaterOutputStream.java:241) ~[?:1.8.0_25]
at java.io.FilterOutputStream.close(FilterOutputStream.java:159) ~[?:1.8.0_25]
at java.io.FilterOutputStream.close(FilterOutputStream.java:159) ~[?:1.8.0_25]
at net.minecraft.world.chunk.storage.AnvilChunkLoader.func_183013_b(AnvilChunkLoader.java:243) ~[atj.class:?]
at net.minecraft.world.chunk.storage.AnvilChunkLoader.func_75814_c(AnvilChunkLoader.java:220) [atj.class:?]
at net.minecraft.world.storage.ThreadedFileIOBase.func_75736_b(SourceFile:37) [bbu.class:?]
at net.minecraft.world.storage.ThreadedFileIOBase.run(SourceFile:30) [bbu.class:?]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_25]
[11:20:07] [File IO Thread/ERROR]: Failed to save chunk
java.lang.IndexOutOfBoundsException: Index: 1546, Size: 1378
at java.util.ArrayList.rangeCheck(ArrayList.java:653) ~[?:1.8.0_25]
at java.util.ArrayList.set(ArrayList.java:444) ~[?:1.8.0_25]
at net.minecraft.world.chunk.storage.RegionFile.func_76706_a(RegionFile.java:226) ~[ath.class:?]
at net.minecraft.world.chunk.storage.RegionFile$ChunkBuffer.close(RegionFile.java:356) ~[ath$a.class:?]
at java.util.zip.DeflaterOutputStream.close(DeflaterOutputStream.java:241) ~[?:1.8.0_25]
at java.io.FilterOutputStream.close(FilterOutputStream.java:159) ~[?:1.8.0_25]
at java.io.FilterOutputStream.close(FilterOutputStream.java:159) ~[?:1.8.0_25]
at net.minecraft.world.chunk.storage.AnvilChunkLoader.func_183013_b(AnvilChunkLoader.java:243) ~[atj.class:?]
at net.minecraft.world.chunk.storage.AnvilChunkLoader.func_75814_c(AnvilChunkLoader.java:220) [atj.class:?]
at net.minecraft.world.storage.ThreadedFileIOBase.func_75736_b(SourceFile:37) [bbu.class:?]
at net.minecraft.world.storage.ThreadedFileIOBase.run(SourceFile:30) [bbu.class:?]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_25]

Anyone have any idea what I can do to fix this?

vanilla or forgesponge? Give version info for the people with mad-skillz here.

if forge, using vanilla blocks, or a mod block? (Assuming you maybe get the error after placing some, but not likely, it would appear to be a saveing event time step not a response to your placement…)

Using any mods that themselves place or break blocks via mechanims - drilling machines, assembling bots, etc? It seems more likely that something programmatically placed /changed a block and botched up a location that the map cant represent when saving.

I made a mistake. After posting this I went to do some tests such as taking out sponge and other files. Turns out the issue was the world file and not Sponge, Forge, Pixelmon, or any of the other stuff in here. Although it is regrettable that the world file wont work Im probably in the wrong forums.

Although if any of you are still able to help is it just 1 chunk or the whole world. Because I could just delete those chunks if I need to. (Do you know the file ID name of the chunks that are botched so I can grab a backup of them and restore it??)

It probably is just one broken chunk. Unfortunately it does not have any coordinate information so I cannot tell you which file is corrupt. Are there any crash reports generated when this happens? Those would have more information if there is one.
Otherwise, if you have backups of the world then just restore to a point where it no longer happens.

No crash reports. However when I walk in game I know where I am that its not saving. Can I use the in game cords to figure out the chunk file(s) that are corrupt? Also I dont have a backup so if this does not work il probably have to make a new world.

You can use Dinnerbone’s coordinate calculator to get the region file for the world position:
https://dinnerbone.com/minecraft/tools/coordinates/