I know this is an old thread, and someone else may have already left a similar comment, but I felt the need to reply to your question with: you actually want to apply the concept of "plausibility" to the Star Trek universe? Good luck indeed.
Same problem here: the commander rank science ability on my Dyson Surveillance Science Destroyer shows up as available (and slottable with a BOFF commander rank power) in the Space Station section, but in the HUD this ability does not show. In my case meaning I can't use my lovely Memu's Tyken's Rift III. I guess somebody…
This. I wanted to file a bug report on the same thing, but for some reason I get an error. Lucky thing you already did it. I took me ages and a lot of frustration to figure out that it was indeed my ship's sensor analysis that kept me in Red Alert status (and thus unable to leave the system or receive a mission update)…
I realise this is an old thread, but since I got stuck on the same part of this (seemingly impossible) mission myself, experiencing a level of frustration similar to that expressed by the OP, I thought I'd put in my two cents anyway. Especially since I managed to solve the problem. I attempted to complete the first stage…