[*]The Warg attack.
[*]Aragorn's pseudo-death.
[*]Faramir turning evil, seizing the ring, and carrying it to Osgoliath, only to change his mind again for no clearly explained reason.
[*]The Ents being stupid and hasty, rather than slow and wise, and so needing to be tricked into attacking Saruman.
[*]Saruman's death.
[*]Various bits cut out, including the cliff-hanger ending we should have had with Shelob.
[*]The introduction of the Ents is clumsy, because certain key sequences were cut from the first film involving the Old Forest and Bombadil.
[*]Little things like Aragorn and co actually attacking the white stranger they think is Saruman, where in the book they realise it would be unethical to do so.