I think there is another thread discussing the glitch, and it almost always affects top floors and builds with somewhat complex roofing. Lots of people have been having the glitch. When you have the glitch, you can't manipulate the wall in any way. You can't delete it, paint it, move the room, or anything. If you click on it, you get a red box that says "Wall doesn't exist." It makes the entire third floor (the usual one affected) unusable practically. And because you can't delete it the walls or the room, you often have to start over from scratch because it's just stuck there.
I am convinced now because of @Fischio7, that this is a conflict with roofing. I think walls associated with roofs (those ones that are placed with the roof) conflict with the real walls. And the game ends up getting confused as to which walls are real and which are associated with the roof segments, especially if they line up on top of each other.
So now I have a new house rebuilt with no roofing. I'm saving the roofing to be placed until the end. That was always a no-no in The Sims 3, because roof placement was blocked by having objects in the room. It seems like that's not the case with TS4, though. At least in my few tests. It may mean that I have to build differently now--in reverse--saving the roof until last instead of doing it first. A bit complicated for figuring out which windows will look best.
Even then, though, I expect that once the roof goes up, the walls will become glitched again, so I have to make absolutely sure everything is just the way I want it.
I'm hoping they get this fixed soon. This is the most annoying glitch for builders I've ever encountered--rivals the disappearing ceiling tiles in TS3 that would pop up elsewhere on the lot floating in mid air. It seems like modern builds with flat roofs or very simple roofs aren't affected. You might not hit up against it with the modern builds because the roofing is different and less likely to conflict with the real walls. I had no issues at all with my modern build, and it had completely flat roof sections. A Victorian, on the other hand, can be a real beast.