It tends to bug when you try and interact with the prisoners while in combat. I had to drop the mission and start over, then I killed all the guards, and after I was out of combat then interacted with them and it worked just fine.
It is slightly bugged, like slightly pregnant?. There is a bunch of scientists to the left, behind the two buildings right before you reach the final scientist. You must free those behind the buildings before you interact with the final group.
I'm lucky my fleetmate discovered this on his own.