Bug #1: As the topic says, its about losing the control over your fighter planes.
It happens every time when you engage with another fighter (CV's or cruiser's). You can't disengage whenever you want, and even when your fighters are out of ammo, they still can't return. When the enemy fighters are also out of ammo, then the fighters just stay there and do nothing, because none of them can return.
Bug #2: In this situation, when none of the fighters have any ammo and a ship kills one of the squadron, the other is stuck there. It became invulnerable and unable to control, can't recall and can't kill it, so effectively losing the fighter a squadron.