My aunt (who, for the record, has yet to be swallowed by a space-time crack) lives in a house with a full-fledged staircase leading up to a low attic.
Uhm, Amy says her Mom used to cut faces on apples.
She remembers her mom.
Yes, I know. And as pointed out above, she also mentions her aunt later on. However.
Logically, if Amy's mother had been taken by one of the cracks, Amy would have ceased to exist too. But in that case the Doctor would never have met her, and never have experienced the events leading up to the explosion that caused the cracks, so there would never have been a crack to swallow her... hello, grandfather paradox.
So what I suspect is that Amy's life "doesn't make sense" because she's caught at the heart of this paradox. Her family has disappeared, but she still remembers them, or some of them, vaguely, still lives in the house full of empty rooms that they ought to be occupying. She had a mother-- obviously, everyone had a mother. But now she lives with her aunt-- her aunt, who either abandons a seven year old at night or sleeps through a phone box crashing outside her window and a strange man eating half the food in her kitchen.
I know: all this sounds less clear-cut than the "never have existed" aspect of the cracks. But look at "The Pandorica Opens." If Rory never existed in linear time, why is there still a picture of him for River to find in Amy's house, and why are her memories of him part of the psychic residue the alliance used to construct the Pandorica scenario? The rules of this, if there are any beyond "what works best for the story," are far from clear.
Or maybe I'm wrong, and Amy's aunt is just a terrible guardian who happens to be out of town during the 2008 portion of "The Eleventh Hour." We'll see.