I was running a mission as a pirate, and, while scanning, got the message that there was a pirate vessel. However, it turned out to be a Federation CAR+. I'm not sure if this is a bug or if my science officer is a retard. It has happened a couple of times, though.
I'd like to recommend a change to a couple of scenarios. In the one where you buy and sell from another pirate, it might be a cool option to be able to attack the other ship. You know, the old "keep the money and the goods" trick.
In the mission where an empire naval ship calls you over for inspection, you should have the option of blasting him, even after he says you're clean.
These are just suggestions, though. Overall, I'm enjoying these new missions enormously. Dave, the drinks are on me next time you're on board the D.P.S. Rorschach.