In the first episode, Amelia Pond had a crack in her wall. This was a crack in reality, allowing Prisoner Zero to escape. The Doctor used his sonic screwdriver to open the crack wide, which would allow it to be closed again. The crack opened and closed...supposedly End of story.
So when the Doctor came back for Amy years later inviting her to join him, we see something that appears to be the crack showing up on the TARDIS' scanner. This is at a point in the dialogue where the Doctor is saying that the only reason that he wants Amy along is because he is lonely. Then he shuts the scanner off. He didn't want Amy to see it. Was he lying about his reason?
So perhaps Amy seems to have something to do with the crack(s).
From the first season on, we get to see a little of the companion's life, family members, and jobs. Not so with Amy Pond. We get a missing aunt, her house which seems to have been neglected over the years, and a man she was going to marry who may or may not be that orderly from the hospital. We do get to see what her job is though: she works for Kiss-O-Gram. Perhaps Moffat is going against the usual narrative.
I don't think so. I think that the TARDIS was drawn to the crack and the Doctor knows more than he is telling.
And Amy Pond is smack dab in the middle of it.
"The Beast Below" aired on BBCA Saturday. Note that in the first beauty shot of Starship UK, there was no crack. In the last beauty shot at the end of the episode it's there.
"The universe is cracked. The Pandorical will open. Silence will fall."