I just finished one game. Towards the end, I built a couple of fighters and a bomber. When I instructed the fighters to patrol above a city, they just disappeared. When I told the bomber to sleep until activated, I could see mention of the bomber if I let my pointer rest on the city, but there was no way I could activate it. Perhaps the game goes nuts if you already have a land unit in the city? But in that case, it should simply refuse to host the aircraft there. Also, the aircraft didn't disappear/become inaccessible until I had issued an order to them.