I've had similar issues, on the taxi bug, I think I found out that the first group placed in the mission editor will spawn in the 4 forward parking spots that can obstruct the taxi way to cats 1 and 2. The workaround is to make sure that those 4 spots are a 4 ship and that they are placed first so that they will launch first.
Another issue I've had, as others have reported, is that planes will park in front of the island when the elevator is occupied when you have a large number of planes landing at once, causing them to foul the deck. Also a plane on the elevator taxing into the hanger glitched up onto the flight deck and parked in the middle of the wires... which also fouled the flight deck. For some reason I do not have a track file for this mission, but as it was taxing into the hanger, as soon as it got inside, it teleported through the deck.
