Had a similar situation, I thought it was because I did a detour to get the ore node, but I think now that it's related to the NPCs taking too long to get to the elevator. I replayed it like you did, and killed the bosses a 2nd time, and waited in the elevator for the NPCs to arrive, and they did (with like 1 sec left).. Not sure if that was intentional, like to create suspense or something, but I got credit for the mission on the subsequent kill. Sucks, but at least it saved most of the progress.