Soo I’m just throwing down a lil shack to wait out Star ore … nothing fancy, and yet I can’t put a roof over my head? How did I fudge this up?
It seems you mixed and matched square with wedge foundations (bottom) and then tried to connect them with all square ceiling pieces (top). Try using the same (shaped) pieces on top as you did on the bottom and it will match up like you want.
@DaVice has the right of it, what is above, so below.
the curtains must match the rug, floor and ceiling tiles need to correspond.
What? I’ve just been informed “Carpet matching Drapes” means… something else. 
Anyway, the pattern of each level need’s to be the same.
That said, there are ways around this.
The upper floors need not actually be connected to the lower floors. Creative use of pillars can make very interesting (and historically accurate) build’s.
Furthermore, while ceiling tiles have very defined personal space, wedges are often more tolerant of overlap.
Besides, two squares with two wedge offsets are the same distance regardless of whether the wedge offsets are on the outside or inside of the walkway.
But those are probably not the techniques you want to invest the time in for a simple meteor processing facility.