The reporting cite "creative differences" which is to me is the same as when a politician gets out of the race because he or she wants to spend more time with his or her family. It's usually bullshit.
Here's what she said about the film and the studio (both sides say the parting was amicable) just a couple of days before she departed the project.
The Marvel guys are so brave in terms of who they choose overall, and I don't think they had any pause about me being a woman.
It would have been great had a woman been able to go the distance and helm a large scale big budget superhero flick. Guess we just have to wait a bit longer.
'Thor 2' Director Patty Jenkins Exits (Hollywood Reporter)