This has likely been brought up already, but i figured another thread wouldn't hurt, because its a fairly common, and highly annoying bug.
When doing a mission with a friend, if one of us happens to take to long in the loading screen, or disconnects as the mission completes, starts, or during any part of it at times, the mission bugs out.
It will tell you to do parts of the mission you already have done, or wont let you complete it. After a while, it resets completely, and you have to do the whole thing over again.
This has happened on every mission ive done with a friend. Especially one that he didnt have yet. A shared mission bugged out the worst.
Usually the person who is lagging will have to redo it. But in this case, my friend and i completed the starbase 24 science team rescue mission, and he left before we could escort them. I couldn't find the rally point, and ended up having to redo the thing myself, even though it was my mission in the first place. I had to share to get him to see it.