This is an issue I commonly come across. MANY times I walk up to a place where a door should obviously be, but i cannot see it. Usually loading a recent save will take care of this. Also, if you go somewhere else and come back a while later(preferably saving and loading a lot) it should reappear. As I have said this is a common problem for me and should be included in a patch. It never really happens to any specific door. The first time I played through the game some turned invisible. Others turned invisible the next time. Its very very annoying.
