When Phil admonishes Hercules, "Don't let your guard down because of a pair of big goo-goo eyes," he's clearly mouthing the word "blue" instead of "goo-goo." Meg's eyes were originally going to be blue, but later on they were changed to purple to match her dress.
When Hercules destroys the marketplace near the beginning of the movie, the pillars start falling outwards from the center of the circle towards the entrance of the marketplace. In the next part of the scene, the pillars are collapsing inwards towards the center of the circle and fall on each other before they crash on the pottery vendor.
When Hercules and Meg are talking after their day together, Meg is wearing a shawl. However, when she turns to talk to Pain and Panic disguised as birds in a nearby birdbath, her shawl is missing. It is there again when she is talking to Hercules.
During the scene with Megara and Hercules by the fountain, the armless statue at the end changes into a man and a woman holding a ribbon between scenes. Also, during that scene, Meg and Hercules change locations around the fountain and the statue rotates with them.
Since this film is only an adaptation of the myths it is understandable for there to be quite a bit of artistic license taken with the stories. Any differences between this film and the myths belong in the trivia section of this site.