I'm guessing that your problem is the unending waves of fighters. Basically, if after the Avenger returns, you kill all of the other fighters, you can autopilot out. Once the Squid fighters show, the only way out is to run away from the fight until you can autopilot.
When Avenger returns the fighters keep on coming, especially the Devil Rays. Took advice to run when Avenger returned. Landed, Bingo for fuel and weapons. But, heck! At my age I'll take getting home with only 8% damage to the ship.