I just had this problem, but in a different mission. Sorry I forget the name of the mission and system at the moment. It was th Episode mission in romulan space where you visit the destroyed planets from the supernova, and have to deal with Remans.
I cleared the entire mission, and when it said "Depart system" I did. But when I reached sector space, the whole mission was reset back to the start.
I had the same issue with the Tephrei System. I found that leaving your team, dropping the mission, exiting the game, logging back into the game, and then entering the system again did the trick.
I think there is an issue with the mission not completing if you don't scan any of the containers or whatever, or maybe it's just the last container. I had to do what I mentioned above twice b/c the first time the team completed the mission before I got to do anything so I made sure the second time I actually scanned something.