I figured Amy and Rory helped them off the Ship like Brian before they returned to the Doctor. Didn't the Doctor say, get them and yourself to safety or something to that effect?
You could still see them when they ran for it at the end.
I presume they were being experimented on but it was a story thread that was undeveloped.
The surgical drones or whatever they were, were gas mask face creepy though. I liked them.
My guess is they were already dead - harvested by the "drones" and autopsied on to determine the most vunerable points of human beings. Freshly killed too, as the "drones" had been at their grisly work for months and would had to replenish their "stock" as the bodies decayed. Evil Hologram Guy had the info he wanted (go for the heart), he just didn't bother to shut them down and they continued cutting people up on autopilot. They just hadn't gotten around to cutting up Brian yet when Rory showed up.