One that I spotted in The Eleventh Hour that I was sure meant something, and then came to nothing by the time of TBB, was that there were three stories in Amy's house on the inside, but only two on the outside. I suppose it could mean something later on or might just come down to filming in two different places, but I felt sure that it meant something
I wondered about this for a while, but someone cleared it up on GB fairly satisfactorily. There's a glimpse in one of the Confidentials, I think the 11th Hour one, where you get a shot of what's what. When the Doctor was chained to the radiator the crew had to film from the top of those stairs, you can see that the door at the top of them opens strangely, kinda like an attic door rather than a normal one. So the 3rd 'floor' is actually an attic room, it's just that it has a proper stairway rather than a ladder. My brother has recently put the same kind of set up in his house as they needed an extra bedroom when my nephew was born last year.
If you look at the roof from the outside though, it only has the tiniest of slopes to it. Not big enough for an attic room. It could be that (as someone said already) they filmed in two different places but if the stairs were to be significant, I would say the outside of the house being the size it is could mean there is another hidden TARDIS on the roof maybe?
