Problem/Bug Corruption under the radar/Out Of Memory

I'd like to start out saying:
I KNOW WHAT "java.lang.OutOfMemoryError: Java heap space" MEANS! (Java Runs out of memory due to using more than allocated memory specified in my startup script.)

My problem leads to Minecraft Server running out of memory.
I've had some problems with my server (the hosting server computer) HDD/SSD filling up to 100%.
This leads to Minecraft having no where to store what happens in the world, smaller and smaller pieces of information is saved until it breaks and crashes.

This further resulted in that the chunks where player who was online at the time of first crash can't be visited and probably many other chunks too.

So my solution was to use programs like "Minecraft Region Fixer" and "MCEdit".
- MRF didn't find anything and MCE have update a lot since I last use it.

Back to the Java error. This only occurs when said player joins the server or another user is visiting the chunk.

In order to reproduce in my world:

1. Player enter chunk.
2. Tries to load chunk (visible for any observer).
3. Minecraft Server "Encountered an unexpected exception"
4. Java runs out of memory.
5. Crash Report Saved. (Include underneath).
6. Minecraft Server stop and save everything under 2 seconds.

I run:

• CraftBukkit version git-Spigot-db6de12-d3e0b6f (MC: 1.8.8) (Implementing API version 1.8.8-R0.1-SNAPSHOT)
• Minecraft Version: 1.8.8
  
• Operating System: Linux (amd64) version 3.2.0-4-amd64
  
• Java Version: 1.8.0_66, Oracle Corporation (64-bit)
  
• JVM Flags: 2 total; -Xmx2048M -Xms256M
  
• Plugins:
  • Bed v1.0
  • PluginReloader v1.3.1
  • NoSpawnChunks v2.0 (Build 142)
  • DisableRespawnScreen v2.0.0
  • ChatFeelings v1.6
  • PermissionFinder v1.2.2
  • PermissionsEx v1.23.3
  • FixChat v1.3.4
  • PTweaks v6.0.15
  • LagPlugin v1.6
  • ChatEx v1.3
  • GlobalTrashCan v1.0
  • ToolRemains v1.5
  • RightOnSpawn v1.2
  • BetterClocks v1.0.2
  • CrashNotifier v2.1.2
  • ProtocolLib v3.6.4
  • LegendaryMessages v6.0.3
  • GetPerms v1.1.15
  • RunAs v1.0.1

Crash Report: http://pastebin.com/nGAkMDFt

If I wasn't clear, I'd like to know more ways of searching for "broken chunks".
Because ain't nothing else wrong with my world.
File permissions - OK
Plugins - Dosen't matter
It's "lag free" to the point of no return (entering such chunk).

Only way the save people from this disaster has so far only been to force teleport the players, restart server and hope they did teleport.

Many hugs and kisses, AminecraftPlayer

Update:
I've saved all players by editing their playerdata file with a NBT Editor
And my "workaround" for the "broken chunks":
Whenever someone steps into one

1. Open the world with MCEdit
2. Go to player
3. Remove the chunk the player stands in
4. Edit the players NBT by setting its position to world spawn.

EDIT by Moderator: merged posts, please use the edit button instead of double posting.