I had it happen to me on the mission where you rescue Ze'mara, and now the Everything Old is New mission where you have to go back to the 23rd century at the Drozana Station. I complete the mission, it gives me the "Mission completed" music, and says something about returning to my own time, I.E the present, as though I had completed the mission and was going to hail Starfleet after I clicked Yes like every single other mission.
But unfortunately, when I got back to the present Drozana Station, my mission only said, "Go to the Drozana Station 23rd century" or something like that. Now I have to do the mission ALL OVER AGAIN. Needless to say, this is incredibly annoying. It is very time consuming, and while I should be leveling up and getting on with my game, I am stuck repeating lengthy missions a second time. Ridiculous!
Yup, happened to me on 'second star to the right' mission a couple days ago, but was able to claim mission reward twice as well so It wasn't a total waste of time. On exit from rewards screen was immediately drop back into mars system for a replay.