First is the mission text for the first half of repelling the Fek'lhri invaders of the ship. The map was reduced for 'streamlining', but 'Assist Crew Quarters'/'Assist Medical Labs'/'Assist Officers Quarters'/'Assist Mess Hall' remains on the list.
Second part of the ship mission on the other hand has a different kind of problem. After helping the Emperor, character is able to go through dialogue with Kahless, and you are able to click on Beaming out. The character is now on the ship in Sector space, with the mission 'Engineered Hostilities' available.
I tried this mission a number of times, and the results are the same.
(edit: thought the special enemy for Klingon Recruit was there, but it was just a big Fek'lhri, most likely I'd have to get past the the second part of the Emperor's ship to get to not only the end/completion of this mission, but also the KR mission.)