This bug is game breaking and very easy to reproduce!
Enter any exploration espisode, exit to sector space then click on the pop-up to continue the mission. It WILL randomly put you in another mission and then once that one is completed the previous mission will stay up and when you go back it puts you in that same mission that you just completed that wasn't even the first mission you had. I hope its not just my account, but when I had a klink it was doing the same thing, EXCEPT when you get to the next zone pop-up (i.e. Beam Down to Station) if warps you to another instance that is half complete with no enemies in it. Please tell me there is a fix for this and a Dev response on what is going on would be great!