I had this very same 'confusing' issue the very first time I played this mission many, many months ago.
This time, it took me 1.5 tries on the mission to complete it (which is a lot less than before heh).
I do not know what happens -- maybe I missed a prompt/console? Maybe the mission wanted me to leave the system and re-enter, but I kept going? I'm not sure.
At first, I was checking off parts of the mission in the journal, but when I reached the 3rd part, it didn't complete, and although I did other parts of the mission, no credit was awarded, and it wouldn't complete.
After I beamed out, I had the option to 'continue:' , which I did, and watched the mission journal for updates.
I ran into only 1 more snag later on my second time through this part. At one point, I was offered the option to beam out, by the mission text, when I still had 1 thing left to do on the base. I'm not sure if that's what did it or not. Something is just a little off on this mission.