Entity Issue

So i am helping someone with a modpack they are making and having a hard time trying to figure out the issue that is going on within a dimension

so once you play the pack and get into this dimension after you have been in there for around an hour or more it seems like it is going corrupt by not being able to place blocks within certain chunks

but after i have used MCEdit on the world there is over 1700 witches that has been spawned into these chunks but they are completely invis and you are unable to kill them 

here is some of the info i have gotten from the world with MCEdit

here is doing an entity scan

this is from the inspector showing a list of entities

less than an hour old gaia dimension. holes in stone are spots block cant be placed
https://i.imgur.com/xegf2ad.png

here is a log if running the kill command to try and kill the witches (/kill @e[type=!Player,r=3])

https://www.dropbox.com/s/l9urg8mokrkmskr/latest.log?dl=0

also here is a the debug log at the same time the kill command was ran above

https://www.dropbox.com/s/wfw7cf6n1vejigq/debug.log?dl=0

then here is a little video of using tnt in the effected area unable to place blocks

https://streamable.com/kvj59

so would anyone be able to suggest something on how to find out what is going on like through a mod to use or some other way