The first aspect of the film that was misrepresented was the charactors themselve. Slughorn, as depicted in the novel, is a somewhat dark many who himself is not sure with whom to side in the wizarding community. In the movie though, he is portrayed as much more loveable and jolly. While this is a not a major difference, the character of Dumbledore was. If moviegoers recall, at the end of "The Order of the Phoenix" Dumbledore admitted to Harry that he had been wrong in the way he tried to prepare Harry for the upcoming challenges. Dumbledore response in the "Half-blood Prince" novel was to be much warmer and closer to Harry. In the movie, however, Dumbledore comes off as being more cold and distant. This was a huge turnoff for me.
The second major area I took issue with was the speed of the movie. The film seemed very hurried. I understand that this is because of the sheer length of the books. However, the rush to move through scenes really distracts the viewer from the storyline. It also presents a horrible Catch 22 - If you haven't read the book then you have trouble following exactly what is going on in the beginning as no explanation is given. If you have read the books then you notice the many drastic scene changes and you really get a rushed feeling.
I believe, however, that the biggest disappointment was just the sheer lack of anything happening. Sure, there was an eventful scene at the end, but the only things before that were an overdramatic high school love story and a feable attempt at explaining what was supposed to be going on. The real problem with the sixth movie is the first five movies. So many details and characters were left out early on that now it makes telling the story (at a level those who read the books would like to see) impossible.
