When Scooby and the gang are in the moon level of the game, when Velma says "Remember what Eric said; We need to find the box of Scooby Snacks", Daphne's voice was heard, but Velma was the one speaking.
At the ending of the film when the gang meets their cyber counterparts, you can tell the real Scooby from the cyber Scooby by the color of their collars (red and blue). However, there are a couple of errors. In the scene where the monster goes over the water flume, both Scoobys wear a red collar in one shot. In a later scene, when the gang stands outside the arcade, Scooby's collar changes from red to blue between shots.
When Scooby and Cyber Scooby are running away from Jaguaro on the carousel at the fairground they start by running against the spinning of the carousel but in the shot from further away they are running with the spinning of the carousel.