Since I installed the 1.1 patch I've had this odd and very frustrating bug. My ships tend to override the commands I give them.
Examples:
-> I tell my fleet to attack a nearby ship (within range of fire) of another fleet. When that ship is destroyed, my caps change to another ship (as they should do). But all my frigs and cruisers stop fire and just follow the fleet command cap without fireing no matter how close the enemy ships are.
-> I tell my fleet to retreat to another planet because of an overwhelming enemy fleet. But for some reason a few ships (most often the caps) decide they wanna play heroes in some strange way so instead they turn and fly the other way which gets them blown up once the main part of the fleet is gone.
-> I tell my fleet to go to one side of a grav well. Halfway there they turn around and go back...
Overall, all my ships have a tendency to remove the current command and return to the last one which is most often is sitting still; sitting ducks. Sometimes they just make up a command of their own and go for that.
This don't happen every time I tell them to do something, just sometimes. But it seems to occur more often the larger the fleet they're in gets.
Anyone else have this, or know a solution? It'd be very appreciated 
Oh, almost forgot. In case it makes any difference, I always play SP, never MP.