This is the only one I can offer a possibility for:
I seem to remember hearing stories to the effect that Foster didn’t think Starling would behave the way she behaved in the book. Now, why the original ending wasn’t used once Foster was out of the picture, I have no idea. I didn’t like either the book or the movie (though the movie wasn’t as bad as I expected), so I’m probably not one to say which ending was better. The ending that story deserved would have deserved a better story.