Don't think that this happened to me. Does it happen in all of the missions or just one? You can only ever have 10 air units at any one time, and you only have 60 units in total, but if it shouldn't take off command points if you go over this limit.
Well, dunno really. Sounds to me like a glitch. Make sure you have downloaded the patch - maybe this will fix the problem.
Sorry I couldn't be more help!
"Life. Don't talk to me about life." (Marvin the paranoid android).