Sometimes there's weird glitches. Just have to exit out and go again. It will usually take you back to the last checkpoint, but sometimes you just have to bite the bullet and do the whole thing over again.
Unless that's what you've done; then you just have to put in a ticket, and maybe wait until it gets patched or something. I had to do that with the second Cardassian mission - it would drop the mission when I switched maps.