When the police are following the plastic surgeon in California they are using a 4-door car with California license plate 1E49962. "1E" plates are only issued to trucks or station wagons registered to a company.
Towards the end of the movie, when Alex enters Casanova's lair and runs after him he accidentally steps on brittle floor and falls into water, yet shortly later in the scene as he chases Casanova, his clothes appear completely dry.
When Alex is talking to Det. John Sampson, Janell is sitting on the right hand side of Vickie while Nana Cross is on the other behind them, but when Alex turns to walk to her Janell is no longer there and he sits down where Janell was only a few seconds before.
Naomi's boyfriend mentions that the river in Durham offers good trout fishing. The Eno River (which runs through northern Durham) offers no trout as do no other piedmont NC rivers. To find trout you'd have to go to the NC mountains. I found this to be a particularly bothersome error considering that when he said it, one could still suspect that he might have something to do with the girls' abduction, and that his error might be a clue that Alex Cross would later use.
During the final showdown between Casanova and Det. Cross, Casanova tells Cross to "pick up the Glock". However, Cross' gun is a Sig Sauer, not a Glock. (In Patterson's novels, however, Cross does carry a Glock.)