After some battles ok with the carrier, I just got again the warning, for the same reason (inactivity) and I would say, cause the carrier was in movement all time, changing speed, changing route (I controlled between every wave) that the reason of the warning is surely the zero damage to the ships. In the last battle with the carrier, infact, all my attacks missed the ships or, for two of them, they hit the ships but dealing zero damage.
The rules says "The Aircraft carriers are considered to be inactive if none of the following conditions are met: destruction of enemy aircraft, damage to enemy ships and aviation by any means (AA guns, secondary battery, ramming) and loss of own aircraft", so losing your planes (as it happened actually) should work to avoid the warning. It seems a bug.