During "Save a friend" quest - short after you enter the sector (I forgot the name) your mothership is always disabled. You are supposed to do this mission only with fighters. I can disable ship disabling
but I don't want to change original storyline in any way.
About "small bug" - could you send me the saved game just before you get these pilots (or before you enter the sector)? I need more information. It's hard to figure out what's wrong without checking logs. I'll send you my email via pm.