There is a bug in this mission.
This occurs after the Junkyard dog steals a ship. If you attack and destroy the hyperspace gate he is flying towards he will stop with the stolen ship and will not divert to any of the other gates. He can then either easily be destroyed, or just left as he is out of action for the rest of the mission.
If he is destroyed your ship does not revert to your control, nor is it salvageable.