I wonder if it is related to Amy's apparent lack of family. When asked about her parents, she replies "I don't have a mum or dad", rather than they are dead. Was that meant literally.
Then we have the apple - who draw the face, Amy's mum or Amy because her mum used to draw it (not so clear now we know time is being rewritten).
And where is the Aunt - the Doctor arrives at 8:30, is eating fish custard at 9:30, and Amelia is waiting for the TARDIS at 11:30. This seems extremely late for her Aunt to be "out" leaving a 7 year old alone.
The Aunt is also noticeable by her absence later in the episode. Prisoner Zero also never mentions the Aunt (although presumedly has been living in the same house for 12 years) nor does Prisoner Zero attempt to use the Aunt has a template (although presumedly could have built one up as with Amy). The lack of reaction from Amy suggests that her Aunt isn't one of the coma patients.
Also, given that fish custard takes place 14 years before June 2010, it must have taken place in 1996, however the London that the TARDIS is flying over very clearly has the millenium dome and london eye neither of which would have been built in 1996. Of course the TARDIS could have time shifted before it crashed (although this isn't the implication). It could just be an oversight but it seems an odd one given it wouldn't have been that difficult to have done a London flyover avoiding such prominent anachronistic (for 1996) landmarks.
Matthew