i may have this completely wrong but i've always thought that there is something odd about the number of rooms on the 1st floor of Amy's house!

correct me if i'm wrong but doesn't Amy say that there are 5 and the doctor corrects her by saying that there are 6 (the one with Zero in it)?

well unless there is a door to the immediate left at the top of the stairs then i can only count 4 (5 with zero's)

In that second picture there looks to be a door at the top of the stairs, only a horizontal one. There seems to be a keyhole at one side, so I suppose you push it open to get into the loft space. Mighty strange setup though!

Edit - just had a strange experience. Looking at those stairs they suddenly seemed to be going DOWN with a door at the bottom! The tread is all wrong for that, but it makes the 'ceiling' definitely a door, there is a frame.

I don't think we ever see it, but Amy gestures in that direction when she's counting them off.

You can see the door to the immediate left at the top of the stairs at about 23:46 mins in, just after prisoner zero has knocked down the door but before he starts barking

(I'm barking already... but that's another story)

It could be a clue hidden in a more obvious scene. At the end of the episode when facing The Atraxi they see the montage of all the previous would-be invaders of Earth.

"Basically, run." he says and they do. Seeing what he is capable struck fear into them and they just left at the thought of having to face him - possibly therefore the most feared creature in all of the cosmos?