use the mission editor to reposition the ships, the game puts things in the general area but not exactly positioned so if you put a ship right next to land or a dock then you have to leave a buffer zone for randomly being out of position without hitting something.
if need be PM the guy who made the missions telling him whats going on so he can fix them, im sure he wants them to work correctly.
by the way what missions are you talking about? where did you find them?
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