Calibos presents Andromeda with a necklace, which he puts around her neck without fastening it. As she leaves the swamp after Calibos rejects her pleas, she removes the necklace from around her neck, which somehow has been fastened in the back.
When Andromeda wakes up to find Perseus has left for the Isle of the Dead without her, we see her from behind standing and looking in the direction he's gone, and her long hair is tucked in under the blanket around her shoulders. When we see her from the front, her hair is clearly pulled out from under the blanket and blowing in the wind.
During the fight with Dioskilos (the two-headed dog), Perseus slashes its right neck, leaving a large, bloody wound. When Dioskilos falls off the ledge, the wound disappears, and then reappears in the next shot.
Early in the movie when Perseus and his mother are about to be thrown into the sea, a large wave crashes on the shore and clearly soaks/surprises everyone. A second later they change to a close up of the king speaking and everyone is dry.
The two soldiers you see without their helmets (one in Medusa's temple, the other fighting the Scorpion) are none of the men you saw lined up behind Thallo (holding their helmets) ready to begin the mission.
Later on in the movie, when Perseus and his guards are fighting the two-headed wolf, his two guards put a slash in the cheek of the wolf. There is a brief splash of blood shown on the left head of the wolf on the right side of its face. Then a couple seconds later, the blood is completely gone.
A regular white horse is used for close-ups of Pegasus, which has been reported as "obvious". But according to Greek mythology, Pegasus did look just like a horse except for the wings, and the close-ups are mostly at an angle where the wing joints would not be visible even if a real Pegasus had been used.
Differences from mythological sources (including misuse of the names Titan and Kraken) are exempt from being listed as goofs, as are historical inaccuracies (including Roman or medieval artifacts in a Greek setting), especially when caused by reliance on Renaissance/Baroque artistic depictions.
In the scene between Perseus and the Stygian Witches, it can be seen that one of the witches has eye holes poked in the "flesh" that covers her eye sockets as she reaches to grab the crystal eye from her sisters.
When Perseus follows the Vulture carrying Andromeda through the air, there is a shot that shows the Vulture flying over the city. Two peasants can be seen walking up a hill at the bottom of the screen. When Persus enters the screen from the top left, riding Pegasus, the two peasants suddenly disappear and instantly reappear a few steps back, then repeat their walk up the hill. In the much later scene when Perseus rides Pegasus to save Andromeda from the Kraken, the same two peasants are briefly visible in the exact same position.
During the climax, when Perseus is flying on Pegasus to rescue Andromeda from the Kraken, there is at least one shot, when the camera is behind his back looking forward, that is identical to a shot earlier in the movie when he was riding Pegasus in pursuit of the giant vulture. The shot contains not only the exact same rock formations, but the exact same cloud formations. He is clearly supposed to be riding in a different direction in each scene: the first towards the swamp, the second towards the ocean.
Perseus drives his sword deep into Dioskilos, yet when he pulls his sword from the creature's body, there is no blood on his sword. However, it is shown earlier that the sword can slice through marble without being scratched, so perhaps this same power also magically cleans the sword.
When Calibos releases the scorpions from the Medusa's head, there are three of them. One kills a soldier, one is killed by Thallo and one is killed by Perseus. Then the fight ends. The one which killed the soldier disappears mid-battle.
When Calibos stabs the Medusa head bag with his prosthetic hand (a three-tined fork-like appliance), a huge quantity of Medusa's blood gets on it. If Medusa's blood is so caustic as to dissolve a shield made by the gods, why doesn't Calibo's prosthetic also dissolve as quickly?
As Calibos pleads for his mother, Thetis, to exact revenge against Perseus for having cut off his hand and won the hand of Andromeda in marriage, his lower dental appliance can clearly be seen to dislodge as he howls "I demand justice!"