Minecraft thinks the sun is shining through my roof, I can't seem to fix it

The sun shines through the roof of my base

What I expected to happen was...:
The roof should block out the sun

What actually happened was...:
The sun shines through my roof

Steps to Reproduce:
I'm not sure how to reproduce the bug, but I think it's mostly random as it doesn't happen anywhere else. Some of the pictures I provided were taken with shaders, just because it makes it easier to see.