I've had this issue a few times but changing camera angle seems to fix it for me. Its almost like the game thinks I'm trying to make the stairs go lower than the terrain and usually only happens when my build has a basement or an unusually high foundation. You might try changing your camera angle. I think the game is trying to build the stairs into a lower floor that may or may not exist when your screen is pointed in certain directions.
I could be wrong but it does seem to fix the problem for me so ...that's something at least.
