The director took quite a bit of artistic license with this movie, but I think that's OK because it's called Troy, not the Iliad. Although I liked it, there were several discrepancies between this movie and the epic poem. Off the top of my head they are -
1) Achilles was a demigod. He was nearly invulnerable except for a spot on his foot where his mother held him when she dipped him into the river Styx. The part where he gets shot in the trunk full of arrows never happened except, but at least in both the book and the movie it is Paris who killed Achilles.
2) In the Iliad the whole pantheon of Greek Gods were involved in the Trojan War. Ares, Athena, Poseidon, Apollo, and company all took an active part during the battles and fought alongside the heroes. Obviously that part was not included in the movie.
3) Patroclus was Achilles' best friend, not his cousin. Although some scholars believe that they were more than just "friends."
4) The Trojan War lasted ten years, but focuses on the last year or so. The movie made it seem that the war lasted only a couple of weeks.
5) Achilles was not the first person on the Trojan beach. Although he was perhaps the greatest hero on the Greek side he was no fool. There was a prophecy that the first Greek to land on Trojan soil would be the first to die, so naturally the Greeks were hesitant to be the first to land, including Achilles.
That's all I can remember for now as it's been a dozen or so years since I last read the book. Despite the inaccuracies though I like this movie a lot. In fact I even rented it last week.