There should be a button for the ship captain to prevent quick-joiners coming on their ship.
Not only that, that you were doing fine with an AI Engineer, but for example on a Goldfish, a 2nd gunner joins and screws things up. Why do you need 2 gunners, especially on a ship like Goldfish for example? Not to mention that, whenever your "trusted" gunner leaves the middle gun, these people can get inside them and screw every one shot they fire...