Even if you are flight leader, they won't always obey you. They will rather do what is in the mission profile. "Cover me" seems to force them to do just that, but the rest won't make them deviate from a scripted behavior. For instance, a "intercept bombers" mission. If you find it advantageous to not engage right away as soon as you see the enemy bombers, it does not matter: you will hear "yourself" on the radio ordering them to attack and they will. Your actual willingness to keep them from attacking is irrelevant.
Aa said above, it is not an "issue" but rather just how the game works. It is also one of the very few aspects where this game is inferior to Il21946/forgotten battles, where you could actually order your guys around.