When Andromeda wakes up to find Perseus has left for the Isle of the Dead without her, she is seen from behind, standing and looking in the direction he's gone, and her long hair is tucked under the blanket around her shoulders. When she is seen from the front, her hair is pulled out from under the blanket and blowing in the wind.
When Perseus first finds the helmet, sword, and shield, the sword reflects direct sunlight, but when seen from a distance, Perseus is standing in the shade.
When Perseus and his mother are about to be thrown into the sea, a large wave crashes on the shore and soaks/surprises everyone. A second later, they change to a closeup of the king speaking, and everyone is dry.
When Perseus first jumps onto Pegasus to tame him, he lands at the base of his neck. The scene then switches to a long shot, and Perseus is sitting behind the wings which weren't even visible in the previous shot.
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.
In closeups of Andromeda's hands, it can be seen that she is wearing nail polish. However, since nail polish dates back to at least 3000 BCE it comes as no surprise that a Joppan princess might wear it.
A regular white horse, reported as "obvious", is used for closeups of Pegasus. According to Greek mythology, however, Pegasus did look just like a horse except for the wings, and the closeups 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.
Scenery is visible through the flying bird in several shots during the opening credits.
When Perseus is with 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.
Despite her firing several shots, the number of arrows in Medusa's quiver remains the same.
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 Perseus and Pegasus enter the screen from the top left, the two peasants suddenly disappear and instantly reappear a few steps back, then repeat their walk up the hill. Much later, when Perseus rides Pegasus to save Andromeda from the Kraken, the same two peasants are briefly visible in the exact same position.
As Perseus and the three soldiers are walking through the tunnel on the Isle of the Dead, the flame of the torch can be seen through Perseus's head.
As the destruction of Argos begins, heavy winds blow the tunic of a man pulling a donkey on a rope to reveal a pair of modern-day gym shorts underneath.
When Acrisius calls to the gods in the opening, modern dental fillings can be seen in several of his teeth.
When Perseus is invisible, he leaves footprints which are those of modern shoes, not sandals.
When Perseus is proclaiming how Pegasus can make a three-day journey in three hours, cigarette smoke is visible wafting into the upper left of the shot.
(at around 27 mins) When Perseus arrives at Joppa, a blue and yellow macaw is seen. This bird is from Central and South America.
Athena's barn owl hoots like a tawny owl.