One thing that hit me in particular is the Giant's Drink game. The way it was presented in the movie didn't really make sense. The book had the Giant's Drink as the end of a long run of mindgames, while the movie had it as the game's chief purpose.
I also think Ender's motivation in that final battle was better done in the book. There, IIRC he was sick of the whole school again, and was trying to flunk out Peter style, by proving he was too vicious and callous to be fit for command. He was trying to do something so abhorrent that they wouldn't give him command of a real fleet, not realizing that he already had it. That all made the twist more horrifying.
Speaking of, maybe it was just because I knew it was coming, but I think they telegraphed the twist too much, while weirdly skipping a lot of the more subtle foreshadowing that the book had.
I was actually looking forward to how they would handle the Peter/Valentine subplot, but given the running time issues it's probably for the best that it was cut entirely.