I noticed that the Doctor's explanation about why there was a spaceship in the same place as the sea ship could be a hint. Could the same thing that is happening to the ship be happening to Amy's baby? In one universe it exists and in one it doesn't, just like the ship.

Not as obvious as the Dr's line when Rory gets his Black Spot.

"I mean if somethings gonna kill you then its nice that it drops you a note to remind you"....

And again when they are in the powder room

"We've all got to go sometime"

PLUS - could it be that future Dr has summonned the TARDIS (when the Dr and the Captain go to get it to rescure the crew)and left the Dr we are watching (the one that we assume gets shot in the first episode) stuck back in history? This would tie in with the first scene of TIA where he is seen through time (middle ages, World War, Laureal and Hardie etc) *and* also resolves the question of the missing TARDIS. There was only one TARDIS in the first place.

Possible?