I've had a few issues with these two missions myself most chiefly being this. After barely successfully raiding all four freighters before they warped out I still get a mission failure. I hadn't don this mission again since till the other day when my Lt. Commander Friend and I ran it (i was a captain 5 matching level) and to our annoyance the civilian escorts were damage sinks. Even with me unmatching level and going full Captain 4 agro on them with their Lt. Commander 5 or so levels they wouldn't go below 50% health. There is something very wrong with these missions.