Weird Mysteries While Playing!?!

I'm not entirely sure what to make of your 'puzzle floor' problem without an image that shows what it looks like. I have had problems with mis-aligning rooms, rooms looking offset because they'd actually ended up unintentionally on different floors, a whole lot of shenanigans going on when accidentally removing floors, having higher than short walls on the first basement level while also having a foundation, and rooms within rooms when they get shuffled around. Sometimes I apparently just want to make a complicated build which the game really don't want me to (or more likely, the developers hoped I would never attempt). Maybe the 'puzzle piece' is the shadow of a piece of it's ceiling that wasn't removed in relation to the rest of the room, even though there aren't any walls directly around the 'puzzle piece'.