Yes, those are corrupted chunks. Usually they're caused by improperly saving the game such as pressing the exit button before leaving the world or a sudden loss of power to the computer. I've never heard of world edit causing this, but I suppose it's possible. When a mob walks into one of those corrupted chunks, the game thinks it disappears and it spawns another one to replace it, but in reality the first one hasn't disappeared and thus you get duplicated mobs.
Anyway, on to fixing the problem. If you're good with computers and technically inclined, I could walk you through how to fix it yourself. If not, it'd probably be easier to just send me your world (or part of it). If you want to send part of your world, here is a list of the files I would need:
.minecraft/saves/<Name of your world>/MiddleEarth/region/67.138.mca .minecraft/saves/<Name of your world>/MiddleEarth/region/67.139.mca .minecraft/saves/<Name of your world>/MiddleEarth/region/68.138.mca .minecraft/saves/<Name of your world>/MiddleEarth/region/68.139.mca .minecraft/saves/<Name of your world>/MiddleEarth/region/117.-42.mcaOnce those chunks are fixed, you should be able to leave the area and return to have the mobs despawn naturally. If you want me to remove the mobs as well, I would need one more file:
.minecraft/saves/<Name of your world>/level.dat
Please let me know what you decide.
I'm not that good with computers so I'll send you the files. I'll let the mobs despawn naturally. Thanks so much for doing this! How should I send them to you?
If you have discord, that would probably be easiest. You can join the wiki's discord with the widget on the right side of this page.
You could also upload them to a file sharing site such as mediafire or dropbox and then send me the link here.
Edit: Resolved via discord.