In the series 5 finale "The Big Bang", The Doctor supposedly closes all the cracks in time by entering the crack in Amy's wall. If so, how does the crack at Trenzalore still exist? Wouldn't it have been closed with every other crack in the universe?
The Doctor explains it himself, during The Time of The Doctor (emphasis mine):
DOCTOR: I knew. I always knew it wasn't over.
CLARA: What is it?
DOCTOR: A split in the skin of reality. A tiny sliver of the 26th of June, 2010. The day the universe blew up.
CLARA: Missed that.
DOCTOR: I rebooted it, put it all back together.
CLARA: That's good.
DOCTOR: Well, it was my Tardis that blew it up in the first place. I felt a degree of responsibility. But the scar tissue remains. A structural weakness in the whole universe.
It was a remain from that day in the Big Bang when the Doctor rebooted the Universe. The scar tissue analogy actually works great.