This is a good question. All movies take liberties and there is nothing wrong with this. Let me give you a list of differences.
- In Homer's Iliad, the gods are all over the place, in the movie the gods do not play a huge role. This is to be expected, because it would be difficult to depict the gods in a film.
- In the movie Hector kills Menelaus. In the Iliad Menelaus does not die at all. Moreover, the movie portrays Menelaus as weak. In the ancient tradition, he is much more capable leader.
- In the movie, Achilles and other Greeks are inside the Trojan Horse. The Iliad does not mention this; more importantly, Achilles before this action.
- Ajax and Agamemnon both survive in the Greek tradition, whereas the movie kills them off. Also there is a great tragedy about the death of Agamemnon at the hand of his wife.
- The role of prophecy is limited in the movie Troy. For example, Cassandra plays no role.
- Many major characters are not mentioned in the movie, such as Diomede, who plays a large role in the book. Also there is mention of Aeneas, but he is little mentioned in the book. I suspect they may want to make a part two with Aeneas.
To be fair, a two hour movie cannot do justice to one of the greatest books of all time.