I am using a hotas warthog for my joystick which is working great. For some reason though it seems like the wingman commands wont work (Shift-A ect...) Not sure if this has to do with the joystick or what, but I cant program them into my stick and I cant use the keyboard to perform them as well. Do the wingmen respond when you send them commands? I cant remember. Whatever the case it doesn't seem to be working, anyone else having this issue?

They do. But you don't always have control over you wingmen. (For example, if you're the only ship in your flight group but there's another flight group, you don't command that other flight group)