Sorry for sounding stupid or if I missed something but....

I think the cracks all over the universe, including Amy's room, were from the Tardis exploding. That's why the Doctor found that bit of 'shrapnal' from the Tardis door in the episode where Rory died.

well we found out that the cracks where because of the TARDIS exploding but we never found out who or what caused the TARDIS to explode in the first place. So we found out how the cracks where created but not why.