It's a pretty common problem, @Moodbeamy. If the game doesn't consider an area a room, then the roof on that level will clip into it. Based on the pictures you've posted, the simplest solution in your case is probably to 1) wall off that area with the roof protruding through in the front where you have it bumped out a tile and 2) redraw a room around the roofing on the side and then delete the unwanted walls. Another thing to keep in mind is that roofing on other levels won't clip into this level, so you can also try redrawing your roofing from above or below (can work in some cases depending on what the roof needs to look like).
