If I delete the attack cruisers command rather then not attacking them until all other unit types have been destroyed they will circle in attack patterns and not attack if all other units have been destroyed.
Yep, I found the same problem. It also happens if you stupidly put their engagement range lower than the minimum range of their weapon. Or similarly if they get stuck attacking a ship they can’t kill. I sometimes think fighters are either an elite, unstoppable locust horde, or piloted by the fleet idiots (“See that button, fly to the enemy and press it as quickly as you can, no don’t worry about that radar thingy it’ll just confuse you”).
I have also seen that behavior, although mostly with the AI Fleet Fighters. As I don’t use Fighters all that much I just assumed the fighters were providing a moving target shield to the Cruiser they were flying around, and my ships did waste a hell of a lot of shots on the Fighters instead of the Cruiser…