A few things that I identified in Eleventh Hour that together mean something...
There seems to be a bit of timey whimey and weirdness in this episode and I wonder it all means something. If it was just one or two of these things, I would just shrug and move on but so much - I hope that it’s leading up to something.
1) The route the crashing TARDIS takes. In EOT the TARDIS takes off vertically and so doesn’t seem to change time or location, and at the start of this, the TARDIS is still over a recognizably modern London (ie still 2005) and then seems to crash into the credits and then Amy’s garden which is apparently near Leicester and in 1996ish. Why the sudden jump when the rest of the crash seemed more linear?
2) The shed the TARDIS crashes into… - something I’ll come back to
3) The crack in the wall - what caused it and why here? - Again something I’ll come back to. Also how does Amy understand what the alien is saying BEFORE the Doctor and TARDIS arrive?
4) The doctor’s repeated time jumps in the TARDIS without realizing - Although the accuracy of TARDIS steering has always been a plot point, this is the first time recently that she continually makes such errors. Is the only reason the damage she’s suffered?
5) Amy’s job - considering that the old lady despite knowing Amy pretty well wasn’t supposed to know her job (but did), then how did Amy keep it a secret in a small village and for that matter how does a small village keep a kissogram busy? If Amy commutes as seems logical, then how did the old lady see Amy’s costumes?
6) Also the old lady and Jeff have a rather matter-of-fact reaction to the Doctor. Only Rory talks about how he can’t be real? Surely Rory’s reaction is more normal so why won’t the others react.
7) The duck Pond - why does the Doctor single it out?
POSSIBLE SPOILER ALERT
Apparently the production crew built that pond so it wasn’t just a throwaway line and given Moffat’s history of having a strong link between people and object - Madame de Pomp and the ship; CAL as both a little girl and the Library computer and now we have Amy/Amelia Pond and a mysterious duck pond with no ducks?Hmmmm...
END OF SPOILER ALERT
8) Rory badge and car - badge issued in rory’s name in 1990??? A prop error or a clue. Similarly rory’s car has a 95 registration. If not a mistake then that Mini is a classic and expensive. Would a nurse really have such a car?
9) Rory’s supervisor - the female doctor at the hospital - why does she treat Rory that way? After Rory’s been proved right about the speaking, why would you assume that he’s wrong about the other thing?
10) Also why is there a hospital with 8 coma patients in a rural area and this isn’t seemingly something noteworthy?
11) Why is the TARDIS scanner showing something very like the wall crack? Is the Doctor asking Amy along for his stated reasons or is there something else?
12) Finally why does Patient Zero not leave at some moment in the twelve years? Even if he was just laying low to avoid detection, surely after the first couple of alien invasions, he would have been worried about the Earth’s survival chances?
Possible ideas:
The village is local - people cannot/are reluctant to leave hence the staying of Prisoner Zero. This effect is also why the TARDIS had trouble getting it and was delayed both times.
Only people from outside the village will notice the odd stuff - the rest like in Castrovalva regard such things as part of reality. This is why seemingly only Rory and Amy see the weird stuff and react.
There is something in or under or around the duck pond that will explain it.
The duck pond also is reminiscent of the original way to Narnia with the dimensional portals as ponds. Given that Amy’s journey seems to be linked to the journey from childhood to adulthood (“I grew up!” “Don’t worry, I’ll soon fix that.”), something also in the Narnia books and the malfunctioning TARDIS crashed into an old wooden shed - slightly reminiscent of the wardrobe, and we already know from Torchwood that TARDIS problems can indeed affect the environment - I think that the shed is going to have an important link to the TARDIS via timey-wimeyness, either directly by the area having a crack or indirectly via the wood of the old shed which was reused in some way.
One of the series promos has the doctor and Amy falling through the vortex as they’re menaced by various baddies and when the weeping angel attacks, the Doctor pushes Amy away for her own safety and then brings her back. I wonder if that is symbolic of the arc storyline. Are Amy, the Doctor and the TARDIS going to get separated and the shed link - perhaps via another “crack”, instrumental in allowing them to reunite and defeat the bad guy? In fact considering the word Pandorica and the idea that Pandora’s Box released all the evils of the world and we have the TARDIS as a proclaimed “box”, I think the bad guy(s), whoever they are, are going to capture the TARDIS somehow and try to use it to open the duck pond which is some sort of dimensional gate/prison which is keeping something terrible out of our dimension. But right at the end when all seems lost, the doctor’s own link with the TARDIS and it’s own consciousness will combined to prevent it i.e. the last thing in the box prevents the opening.