The first time, I warped out when my Ops officer told me to, after defeating the alpha's ship. It was marked as complete in my journal display under the mini-map. Once out in Sector Space, it jumped back to rescuing the hostages, with a Continue: Hunting the Hunters prompt. Going in, it took me to right after disabling the generator to rescue the first ambassador.
I probably should have filed a ticket, but it was late - especially after redoing that bit!
"Don't let them promote you. Don't let them transfer you. Don't let them do anything that takes you off the bridge of that ship, because while you're there... you can make a difference." - James T. Kirk