When a fleet contains a scout that is set to auto mine sweep, the target priority of the fleet should be mines first. What I am experiencing is having to micro the mine sweeping fleet. If I use gardas, they want to run off after any new strike craft that is spawned instead of mine sweeping. If I use carriers with fighters, same behavior. I lost 40 lrms in one battle when they went chasing a trade ship that had entered the grav well on the otherside of a mine field. 
I would really like them to concentrate on the mines so that I can concentrate on the rest of the battle. If for some reason I want them to tear off after that one new spawned strikecraft, I will micro that instead of clearing the landing zone for my frigates.