when The Doctor runs away with River and the other guy while the others guard Amy, we see a second or so later the Doctor come back to comfort Amy and kiss her on the head. Notice that The Doctor that leaves has no jacket, and the one that comforts Amy is wearing one

Also looking back to the first episode, at the end we see the young Amy waiting as she hears the Tardis.
Possibly two doctors with two timelines happening. The one we're following is the adult Amy that grew up with the Doctor returning years later. The timeline is getting erased because the The Doctor did correct his mistake and went back for Amy as a child.
would be pretty fucking awesome if that was what was happening