Factual error: At the beginning of the film, after Eris gives her speech, we zoom in on a map of the Eastern Mediterranean - and the island of Cyprus is conspicuously missing (it's large enough to be seen on the map).
Other mistake: As they're chasing the giant fish and the ship is bouncing on the waves, we can see in some shots a major design flaw - the ship has no rudder.
Continuity mistake: When Sinbad and his men attack Proteus' ship and Proteus is fighting, the neck of his shirt gets torn. In each shot after this the neck line keeps switching between being torn and not being torn.
