When Scarlett is thrown into the dungeon, she and Selena fight each other. In the over the shoulder shot of Scarlett on the floor and the lighting is off of her, a headband, which is a replica of the one Selena wears, appears out of nowhere. Scarlett was never wearing a headband before or after she ended up on the floor.
When Duke's childhood memory is shown on a view screen, a brown haired boy with green clothes is bullying a bespectacled kid. Another boy runs up with the same brown hair color and green clothes. But his colors suddenly change to blond hair with blue clothes (this is young Duke) as he punches the bully in green.
After Selena and Scarlett are foiled in their rebellion, they are shackled and chained. Selena says "You are very brave", but it is Scarlett's mouth that is moving.
Scarlett had been kidnapped by Destro at the end of part 4 and was taken to Cobra Temple. But when the Joes are around their MASS device in part 5 getting ready to fire it in attempt to stop Cobra's beam, in a wide overhead shot from slightly behind everyone, Scarlett is seen standing there with the Joes with her back to the screen. But since she is still a captive, she shouldn't be there.
During the final attack on the Cobra fortress, Gung-Ho sets a helicopter to "auto-hover" mode, and then he, Snake Eyes, Scarlet and others all jump out, presumably leaving the chopper unoccupied and eventually to crash from lack of fuel.