The second story part of the house where I brought in the top to tilt, I grabbed the edges and clicked extrude edges, centered the little tool, and went to bring them in to connect in the middle. As I was bringing them in together I noticed that some of the edges werent extruding at all or it's just not visible.
All I did was duplicate the lower half of the building which is made out of a polygon, didn't really do much to get to this step of the building. I've actually stopped doing anything to it until I get this problem figured out.

Edit: I figured out my problem on my own, under polygons>tool options, I had "Create meshes single sided" checked