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.