Steven Moffat has explained the timey-wimey confusion,
following the events in The Time of the Doctor.

In the latest issue of Doctor Who Magazine, a reader asks
that if The Doctor prevented his own death,
how could his tomb be in The Name of the Doctor?

Moffat replies: “I’ve often wondered about that. Fortunately
, late one night, The Doctor turned up in person and explained it to me:”

“THE DOCTOR: Changing time is tricky. It’s a bit like a detective story:
so as long there isn’t an actual body, you’ve got a certain
amount of wiggle room – for instance, if the body has,
rather conveniently, been burned on a boat in Utah.”

“Here’s the thing: I can change the future so long as the
future has not already been established as part of my own past.
I can’t rescue Amy and Rory because I already know that I didn’t.”

“But what do I know about Trenzalore? There’s a big monument
that looks very like my TARDIS. There’s a temporal
fissure leading to my timeline. Maybe it’s my grave.
Maybe, one day, it’s my burial ground. Maybe it is
something else entirely, and we got it all wrong.
Don’t know. Don’t plan to find out for as long as possible.”

“The main thing is, Clara still jumped into my time stream,
and ended up helping me through all of my life.
All that is established, unchanged – but there’s wiggle room!”