My biggest issue with this episode is that once again the Doctor shunts Amy and Rory to the side. This week he had no real reason to tell them to search other floors after he'd spotted the scared kid, other than maybe he likes doing this sort of thing sans Amy and Rory. In that case, why bring them anywhere?
It would be nice if for once Amy or Rory were the ones to solve the problem - that hasn't happened all that much this season.
Given the "in the flesh" line this is probably a side effect of the episode having been swapped with the pirates - at this point he would have known Amy was a Flesh copy...