Hey! I’ve had this issue too and it’s really frustrating I found a way to fix it tho. So you press the up arrow button on the right upper hand corner that usually puts the roof top not the actually roof but the flat surface you put your roof one - pick a tile or floor patter and right click shift so it covers the entire next level in that pattern, add rooms to this level make sure the rooms are in the same shape as the first level - I then went through and deleted the walls separating the rooms making it one big level just leaving the mane walls and then I hit the down arrow button and placed my stairs and it worked that time without making everything dark and blue 😁 hope this helps!!
