Still I can't find the last spot. I'll try to begin a new savefile later.
If you've cleared all missions and the game tells you you've got all clear points, then it's officially a bug.
I know what vids 1 and 2 are. Unity has trouble putting sprites this close to meshes. I'm using sprites because I couldn't get proper decals to work. Vid 3 is to do with the boundary collision mesh, I'll see what I can do about that. Vids 4 and 5 are just waypoint goofiness and should be much easier to fix.