regarding the "exploding ship bug"
maybe you already fixed this bug, but just in case:
in my opinion it is a bug in the ship/shuttle automation. -> when a ship has launched shuttles and is beaten, the shuttles are destroyed in the same moment their "mothership" is exploding, regardless their status. Thatīs EXACTLY what happens to your team mates AND other ships/stations as well: getting destroyed when something explodes.