Well, I tried to make an airplane with a lot of different parts. I had it going well until I undo/redo while switching between Edit and Object mode. I really messed up my model but I learned quite a bit from what I did accomplish. 
Long story short, I was extruding edges instead of vertices. So when I filled them there were two overlapping edges. When I moved around the vertices there would be gaps with no faces. To resolve the issue I went back and removed the duplicate edge and re-filled it with all vertices. I am not sure if this makes any sense… but here are some pictures.
