I just ran this mission with a couple guys, and got up to 5 prisoners, with 3 bugged ones. I looked through this and another thread on the subject, and the bug may occur when looting enemies mid-fight. Whether this is the case or not, I don't know, but the workaround we found is this:
Since the story area is tied to one group member, you'll need to leave the area, then find a way to change who that story area is tied to. You do not need to reset the quest. We just ungrouped, then had a different player enter the area, who then invited the other players from inside. That reset the area, and with it, the prisoners. But you still keep your current status in the quest.
And since looting mid-fight may be the cause for the bugging, you should avoid doing so, just in case.