First keycard in the storage room on the opposite side of the stairs/hangar, second keycard is outside hydroponics, third in the captains room.
After you get the third keycard from the captains room to get into the hangar, I got the message "Go back to the other girls" in the questlog which is back to engine room, did you try that? Are you running the 1.0 version?
Replayed up to that part in order to refresh my memory.