[03:15:45 WARN]: java.io.IOException: Stream Closed
[03:15:45 WARN]: at java.io.RandomAccessFile.seek0(Native Method)
[03:15:45 WARN]: at java.io.RandomAccessFile.seek(Unknown Source)
[03:15:45 WARN]: at net.minecraft.server.v1_9_R1.RegionFile.a(RegionFile.java:254)
[03:15:45 WARN]: at net.minecraft.server.v1_9_R1.RegionFile.a(RegionFile.java:191)
[03:15:45 WARN]: at net.minecraft.server.v1_9_R1.RegionFile$ChunkBuffer.close(RegionFile.java:303)
[03:15:45 WARN]: at java.util.zip.DeflaterOutputStream.close(Unknown Source)
[03:15:45 WARN]: at java.io.FilterOutputStream.close(Unknown Source)
[03:15:45 WARN]: at java.io.FilterOutputStream.close(Unknown Source)
[03:15:45 WARN]: at net.minecraft.server.v1_9_R1.ChunkRegionLoader.b(ChunkRegionLoader.java:183)
[03:15:45 WARN]: at net.minecraft.server.v1_9_R1.ChunkRegionLoader.c(ChunkRegionLoader.java:164)
[03:15:45 WARN]: at net.minecraft.server.v1_9_R1.FileIOThread.c(SourceFile:37)
[03:15:45 WARN]: at net.minecraft.server.v1_9_R1.FileIOThread.run(SourceFile:30)
[03:15:45 WARN]: at java.lang.Thread.run(Unknown Source)
http://prntscr.com/bl652i <-- Picture of my spigot verion.

This error is generated only once in a rougly 20 times of my plugin copying a world from a folder in my plugin data folder then being coppied in my worlds folder and being loaded, I do this repeatedly for a minigame and when it occurs the worlds chunks are all funky and messed up, chunks for the map are improperly loaded.