Is this a known bug?
I took on an assassination mission in Ngalites, jumped to the first system and waited for a USS. Got the message that my target was back in Ngalites so I returned. At the first USS there was a green 'conda with the wrong name (so not my target) but he was worth nearly a third of a million so green or not - he was going down.
I didn't get any branch messengers up to that point, so as far as I was concerned, I was still going to be hunting William Rogers after I popped this 'conda called Wraak, but I got the "Objective completed" message instead. When I got back to the station, the rep was applied for the correct faction for the mission, even though Wraak belonged to that faction.