My guess is they were already dead - harvested by the "drones" and autopsied on to determine the most vunerable points of human beings.
Character stuff aside wasn't the whole point of the episode that that was what the Cubes were doing?
And how did nobody in the hospital notice a little girl sitting there all day every day for a year?
(And how amazing was it that out of all the places in the world they could be they were in Rory's hospital?)
And don't forget kids, when Moffat does move on Chibnall's almost certainly going to get his job...