Invisible area that subtracts/hides objects

Here’s video: https://streamable.com/tozqc

What’s going on there? I’m somewhat beginner so try to keep it simple.

EDIT 1: I tried deleting some surrounding objects and suddenly it removed that problem. But I would like to know what caused it? New video: https://streamable.com/127vu

I tried editing my post but it’s not showing?

I found out that deleting one box removed that problem area but I would like to know what caused this. New video: https://streamable.com/127vu