In Clash of the Titans, Andromeda is a brunette, but in this film she is a blonde.
At 40:15 the group is shown as compromising 8 members, but the number remains constant as so later on (e.g. 47:43 or 48:22) , despite having added Hephaestus. Since there was no justifiable event during this time-frame, they should number 9.
There isn't in the Greek Mythology anything like Kraken.
During the battle with the Chimera at the start of the movie, Perseus shields himself from fire shot out of the mouth of the chimera with a wooden door. His hands are gripping the door with fingers going to the front, but at no point does he appear burnt or show any sign of pain.
Since this film is fantasy rather than history, some minor anachronisms are allowed, such as a Greek army using Roman tools or flags. Since many iconic "Greek myth" images come in fact from the Italian Renaissance, anything from up until the 17th century AD is fair game.
In the tomb of Io can be read "beloved wife and mother" in modern English, instead ancient Greek as it should be written. This is done for the convenience of the audience, as is the film's dialogue being in English. Classic Biblical epic films set before the creation of the English language are in English for this same reason.
When Perseus is holding Poseidon's trident while they are talking in the temple, the Modern English word "below" is clearly written on Perseus' arm in black marker.
At around the 71st minute, Agenor shouts, and a gold crown with modern dental work is clearly visible in his open mouth.
During various battles the archers are told to "fire" or "hold fire" also the artillery was told to "fire". The term "fire" didn't come around until the advent of gunpowder powered weapons. The correct command would have been "Loose".
When Agenor says "Oi, Helius! Come meet your uncle Navigator!" - he's wrong. As son and grandson of Poseidon and Zeus (respectively), who are brothers, they are first cousins once removed.