I've only noticed this recently, but it seems like wingmen tend to ignore your orders unless you use the exact same method of command every time. For example, if I order Alpha 2 to cover me and then order Alpha wing to destroy a subsystem, Alpha 2 will continue to cover me while 3 and 4 go off to destroy the subsystem. I have to give 2 a separate, individual order to make it change what it's doing. It's almost like 2 ceases to be part of Alpha wing once I give it an individual order.
Another thing I've noticed is that if I use one of the F5-F12 hotkeys to issue orders, the ships I give those orders to will ignore orders I give them through the regular comms menu. So if I told Alpha to protect my target by pressing Shift-P and then F5, and then tried to press C-2-1-9 to have them engage at will, they'll ignore the second order and continue protecting that target unless I use Shift-E followed by F5.
I don't know if this is an SCP bug, an unfixed retail bug, an intended feature, if I'm just crazy, or if I'm the only one weird enough to frequently switch between the comms menu and the hotkeys, but it can get pretty inconvenient in missions where I have to do a lot of wingman management and things are hectic enough without having to remember exactly what command method I used for every ship I've given orders to so far.
Just wanted to know if anyone else has experienced this.