I had the most problems with the film's final third. Harry and Dumbledore's trip to the caves seemed to come out of nowhere, as did Dumbledore's declaration that he had to drink the water from the podium in which the locket they were after was held. I don't remember if tha's how it happened in the book, but I remember arriving at that location & conclusion in a way that at least felt more natural.

After that, they make their way to the tower and instead of using a charm to immobilize Harry and cover him with the invisibility cloak like in the book, Dumbledore just sends Harry away, and Harry goes downstairs, stops & watches the following scene through cracks in the floor above him. Malfoy tries to kill Dumbledore but realizes he can't. Snape arrives on the floor below & signals Harry to be quiet, which he uncharacteristically does. Snape then goes upstairs & sends Dumbledore to his death. The modifications made to this scene from book to film are terrible, and they partially blow what may be the biggest surprise of the entire franchise.

Afterwards, there is no enormous battle. The Death Eaters stroll out silently. I remember the fight in the book being fantastic, and I personally would rather have had a short scene in the beginning with two guys talking about the horrible things the Death Eaters are doing than eliminate the battle at the end. Harry runs after them and confronts Snape, who quietly tells him he's the Half-Blood Prince. Again, due to lack of attention paid to this plotline, I didn't really care. In the book, he screams his response. The book has Snape screaming and the film has him using his indoor voice. What a disappointment.

And as if this weren't enough, there is no funeral for Dumbledore. It's been cut.