Thought I'd pick a fight with some random Xenos to get on Junkers good side and they just let me kill them. Took a mission to kill Xenos and got hammered lol. The ones on patrol in liberty space won't fight back, am I missing something?.
It depends. The mission level dictates the difficulty and the enemies' shiptypes. If you pick a high level one, it's gonna be tough, they might even have gunboats - no chance in a fighter.
So pick easier missions, the rest is just practice. Or get another player to help you
NPCs not fighting back is kinda normal, but I don't know why they sometimes act like that.