Alright, every model is made of two "models", the one you see and then the one the game sees, which is called collision, and with large complex models those two can be varying a bit, which means you see a model but the game itself isn't, so you can, as it is in your case, fly through parts of the model you see, because the game thinks there is no model.
Well, now you surely have seen some invisible walls on some stock maps, where you can not walk through if you want to leave the battlefield, these are invisible barriers. They are called "com_inv_col16" (or 32 or 64, depending on their size) in your world's common/odf folder, just load them into ZeroEditor and place them just a little under your hangar floor, so that you can walk on them, not the actual hangar. You can also do this everywhere else you need proper collision.
That's it in easy words, please ask if you don't understand all things.
