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.
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. Royalty of the time often used hair dye and other cosmetics to distinguish their appearance from the common people.
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.