Just a couple tips that might help.
First make sure you have a squandron of whatever fighter you want to fly in the mission. I usually make the squadron have at least 12 of the given ship. You can go as high as you like, but if you put more than 24 ships in the sqaudron it can cause floods of fighters to be launched by teh carrier. So first create a squadron of 12-24 ships of whatever craft you want to fly. Make sure that the sqaudron has the same IFF number (usually 1) as your carrier does, then in the carrier window make sure you select the name of your carrier to properly assign the squadron. You should click on the command AI box then so that it is highlighted, but none of the other boxes should be highlighted except this one.
Once you have the squardon, you then create an element made of up 1-4 fighters of the same type. Make sure that you select the name of your sqaudron that you created in the squandron window of the element. Do not assign the element to the carrier only to the squadron. Make sure you highlight the player, alert, and command AI boxes for the element and you should be all set. Hope this helps.