Yesterday, after dying during the final battle in Directive 7, I revived on the fleet, as is normal. Rest of the team was inside and managed to kill the dude while I was loading the fleet. So I want to run back in, but after that loading screen I find myself back in the fleet, and not in the FP. Happens several times. The quest isn't marked completed, and I don't get any loot.

That was annoying, so say the least.

Thats what happens if you release (respawn) during the fight and its finished while you're out of the instance. Next time wait for a wipe or clear before you release. If you're dead and in the instance when they clear it you will still progress the quest.

EDIT: Should probably also mention that the return to fleet thing was because the instance was cleared/locked so you can't go back in.