(Spoilers for anyone who hasn't played this mission yet)
I've tried to run "What Lies Beneath" four times, at least once with a Fed and a Klingon character. I always get to the end, scan the portal, receive the message that the mission is complete and I should beam out. So I beam out. Then, instead of returning to my ship, I'm back on the station, and the mission log says that --OOPS! You Forgot To Scan The Portal!-- And I can't get back to the mission levels; I have to start all over from the beginning.
I just completed the mission in a team. There appears to be a pernicious but unreliable issue causing mission completion to break in general, but it will take some software work to track it down. Essentially, missions resetting seems (at this time) to be random.
Only problem I ever had is where it seemed if you take that federation ship down too low on its health it would cause the npcs in the bar to not take damage. Being these need to replay for limited time items cause burn outs usually after I do them on a character once I never do them again. It's mostly just this limited time item issue just turns me off from doing them when those items are not available.