On Charon's ferry when Io is training Perseus, she ends up lying down on the floor of the boat with coins all around her. The positions of these coins changes between shots, and some disappear completely.
At the end of the movie Andromeda says to Perseus that Argos will need a leader now, but both her and Perseus were facing the other way when her father was killed (distracted somewhat by the humongous Kraken trying to eat them) he was also obstructed by the crowd of panicking people.
When Spyros discovers Perseus as a baby with his dead mother Danae in the casket, Perseus' mother has brown hair. In a later flashback, Danae is blonde. Royal people have always been fond of using cosmetics including hair coloring.
Differences from mythological sources (including misuse of the names Titan and Kraken) are exempt from being listed as goofs, as are historical inaccuracies, especially when caused by reliance on Renaissance/Baroque artistic depictions.