Random black spots in HL2

I've come across a "glitch" I've never seen before and I was hoping someone would know what this is all about as I can't even find any info about it online.

I'm making a map for HL2ep2 and after compiling my map I get very strange black spots in certain brushes. These spots are completely black, and don't react to lighting of any kind, be it light entities or the player's flashlight.

What's even stranger to me is that these black spots don't take up the whole brush, only a subsection of it. In the image below, the brush with the black spot on the right actually extends all the way into the door.
I would imagine this problem as something to do with the fact that that area is a func_instance collapsed into the main map but I can't figure out how to fix this.

If someone could help me figure out what is happening that would be greatly appreciated. Thanks.

Well, this post proved to be unnecessary as I seem to have found a fix for this, but maybe someone else benefits from it if they're having the same problem.

This is the most frustration I think hammer as ever provided me with as the fix is rather weird. All I needed to do was to delete the entire map and save. After that ctrl-z and save it again. And it's fixed. I have no idea why it was causing the error, or why this fix even works because I'm basically deleting everything from the vmf and pasting it back in but I guess hammer is old and I have to just put up with it.

If anyone feels adventurous and wants to investigate this I'd still love to understand what was happening.

Scratch that, apparently this only works some of the time. The rest of the time hammer just does has it pleases.

I actually found a wall that had black spots on the inside and outside faces. The whole deleting and getting everything back in fixed one of the sides, but not the other.

It's really frustrating, if someone has any idea I'd love to hear it.

EDIT: And other times it actually creates completely new black spots. It's just completely random, I can't find any pattern to what is happening.