Black holes in render have me completely stumped, help?

So I’ve never seen something like this before and I can’t seem to find anyone else online who was having the same problem, but somewhere in compositing I’m getting these black square holes popping up (seemingly randomly) in my render. I can’t even figure out where the problem is coming from, whether it’s a compositing bug or an object in the scene causing it.

Here's an example of the problem:

Above is frame 112, and it is completely normal.

This picture above is frame 113, and there’s a huge black square in the middle.

Oddly enough, I found that having the compositor export the image using the file output node gets rig of most of these, but not all. I've also tried rendering this on a spare laptop running a different version of Blender and the result was the same.

This has had me stumped for over a week now, and I don't want to progress any farther in my project if I can't get this figured out. If anyone has seen this before or has an idea as to what could be causing it that would be amazing. I'll include the .blend at the bottom if you want to try something. If anyone has any ideas I'll be eternally grateful! 


I am looking at it but this blend file is a monster.
y so big?

Not really sure, can’t be textures because the resolutions are so low. I’m guessing it’s just a lot of geometry.