sometime it happens as result of this bug, that you cannot control bring out aircraft even if on your screen you can see them.
Dunno from what it depends, maybe de-sync problems with the fight when you click "quit", or even if u dont.
Anyway when it happens is kinda frustating, not being able to control your ships, and as result watching your ships go to death without being able to do anythin.
in the past I have had a similar problem where my fighters are active one round, and the next round they aren't part of the battle. they sit there doing nothing and not absorbing any damage while the enemy fighters are attacking my main ships.
i didnt take any screenshots so i'll try to remember how many details i can from last case.
1° round i clicked on "battle" to send my first commander into fight and then i clicked the formation.
Dunno excactly what happen immediatly after, somethin bugged with timer so i tried to press "quit" and rejoined the fight. After rejoin, i sent out my aircraft (and they was there on my screen). I waited the timer to next round to elapse and few other seconds to pass, but i couldnt understand if my aircraft was out for real or not. So i tried to press "exit" again, and when i rejoined i noticed that my aircraft wasnt still outside. I have tried to wait 15 sec or so this time (After sent in aircraft), but the fight ended on round 4. both my shuttle commander n trasport commander had lost, without me being able to control anythin.
i think this bug is very important to be fixed. For example if it happens during a 5-commander fight in which u invest many resources... frustation would be lot.