2 things:
first, the game will always spawn a random number of ships in port so if your placing ships in port then a mission may work fine many times then suddenly keep getting ships spawning on top of each other. i have had some missions where i gave up and just put a ship somewhere else to avoid it.
second, did you validate the mision?
if you validated the mission and all was ok then its likely you have a game corruption issue. if its mod soup related that can be corrected easy enough if not then you might need to reinstall.
lastly: have you opened the mission files (with windows notepad) and checked to see if two ships are supposed to be spawned (as in a mission creation issue) or if only one ship per location is listed then its game related and not mission related.
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