Continuity mistake: When the bus passes Poseidon and he disappears, the people walking near him also disappear. There is an Asian couple walking from left to right across the shot that should have been still there after Poseidon is gone. Sloppy SFX that sort of spoils the effect of a god being able to vanish.
Continuity mistake: There are several scenes where Percy is shown wearing a watch, but it seems to disappear in the next shot or two (most noticable in the Parthenon scene).
Continuity mistake: Sally and Grover are taking Percy to Camp Halfblood; Sally has her head turned to the right, speaking to Percy. Grover, in the back seat, is looking front as he yells for her to watch out. Sally looks forward, and with a surprised look, swerves left to avoid whatever it is she sees. Then the cow, thrown by the minotaur, comes in from behind, above and to the right and lands in front of the car, a direction in which neither Sally or Grover were looking.