I did not have this happen to me last night but I am not denying that there could be a bug here. Then again how long did you wait? Maybe there was lag involved?
Sounds a lot like the bug found in the Mirror Universe patrol Khonshu Khaibit. Several times I've cleared out the Terran ships at the final stage only to have the mission fail to complete.
Comments
*edit* I ran the other patrol successfully, then ran this one again; the end of mission success triggered the second playthrough.
See this post:
https://www.arcgames.com/en/forums/startrekonline#/discussion/1269385/khonshu-patrol-cannot-complete