<strike>Not sure if I can put this here, but I just ran across this about an hour and a half ago, gave up and tried again just now.
The problem is that the mission waypoint shows at both the originating mission base or what would be the "first" waypoint labelled as the #2 waypoint and the final destination (where the NPCs spawn) marked as waypoint #1.
Here's the screens to give an idea.
The left one was taken first, and then the right one was taken an hour and a half afterwards, after a freelancer restart. Both missions were taken from the Battleship Strausberg, with a Recruit IDed Wraith. I'll give it a few more shots and update if anything changes.
Update: Just tried again, to show that the waypoint doesn't go away when you get to #1.
Edit: Seems like others are having this problem as well, feel free to delete this if it is a common occurrence.</strike>
Indeed others are having this problem as well, I've simply never seen it manifest itself this way. Delete or leave up, I'll chalk it up to lag-based issues.