Fleet Command has one game-breaking bug which has never been corrected in any official patch or fan mod. This bug affects aircraft carriers as well as airfields.
Guide to Avoid Breaking the Aircraft Carrier Deck
During your playtime, you may notice that aircraft will start endlessly circling the carrier when attempting to land, or that one aircraft fails to take off. This is a serious problem: If this happens, you may be unable to launch any more aircraft, and currently airborne planes/helicopters may be unable to land. If you cannot quickly finish the scenario, you are doomed to be without air cover, and any planes in the air will eventually run out of fuel and crash. After much trial and error, I have discovered three causes of this bug, and how to avoid them.
If you order an aircraft that is not currently in a state of “readiness” (5, 15 or 30 minutes) to immediately take off, and then later cancel the launch sequence for any reason, this will break that catapult and prevent aircraft from landing on the deck.
If you need to scramble aircraft that are not in a state of readiness, do not, under any circumstances, later cancel the launch. If you think you may need an aircraft later, but aren’t certain of it, put them into an alert status. This way, if you decide to cancel their readiness later and ready other aircraft, the carrier will remain functional.
If you order aircraft to planes to launch too quickly after the last batch of planes have taken off, this may break a catapult.
Your carrier can launch four planes at once (airfields can only launch one or two at a time depending on the runway configuration). If you have more than four planes set to launch at once, or there isn’t enough time between batches of aircraft, this can break the carrier deck. You must be absolutely certain not to launch more aircraft at once than the carrier/airport can handle, and give some time between launching groups of aircraft.
For example: If you have set four aircraft to launch in 30 minutes, make sure you wait an additional 6 minutes or so before queuing up another group of four aircraft. This time isn’t exact, and I will experiment with it, but I’ve never had an issue with aircraft launching with a 6.5 minute delay between groups taking off, as this allows plenty of time for the aircraft to go through with their prep animations and take off.
Aircraft refuse to land, can take off without issue.
Make sure you do not have any aircraft set to Alert 5 on the carrier deck, as this prevents landing.