What changed about the ending of Gone Girl?

There wasn't that much difference between the novel and the movie. Really, the only difference is that instead of both of them writing their memoirs (so to speak), only Amy does this. The fact they stay together and she is pregnant is identical in both works.

Quoting from the Independent:

In the run up to the premiere, Fincher quoted Ben Affleck as saying of Flynn's screenplay, “This is a whole new third act! She literally threw that third act out and started from scratch," but the author has since played this down, saying the reports following it were "greatly exaggerated".

It seems the original basis for this story was that Fincher was disappointed in the box office reaction to his faithful adaptions of The Girl with the Dragon Tattoo and so supposedly wanted to change the ending. Given Flynn's comments above, it seems likely that these sentiments were either misinterpreted, or never true to begin with.

I have only seen the movie and read the synopsis of the book on the Wikipedia page, The only subtle difference i see from the ending of that to the movie is that in the movie Nick decides to leave Amy when she reveals to him that she killed Desi but decides against it when he hears she is pregnant but in the book it's shown he was ready to write a memoir detailing the truth of Amy's abduction but decides against it when he hears she is pregnant.