I don't know if it does this with any other nation yet but im in the latest era with the Japanese and I have the reisen fighter and 4 bombers on a aerodrome then I try to put the three bombers on the aircraft carrier first no problem there, but after I put the reisen on the aircraft carrier and then the bombers disappear 

Sorry I dont have a screen recorder but I believe I showed enough with the three images here I have the file saved to replicate this 

I also noticed this when I've tried to put any planes on an aircraft carrier. Once they're on there, they don't work correctly. I tried moving them back to an aerodrome and now they just sit there. I can't disband them, can't attack with them, can't patrol with them. Obviously some sort of bug.