Other mistake: When Scooby and Shaggy are in the cafe, Shaggy says "Can you believe the cafe ran out of food but we're still hungry." But we can see food behind the counter.
Other mistake: In the last level, Scooby and Cyber Scooby are on the merry go round, before Scooby sneezes you can see a slight glint of Scooby Doo's collar. They are both green.
Continuity mistake: While the scientist is explaining how the blue virus-monster attacked him and his students, a flashback of the attack scene is shown. However, in this flashback, the telephone wires that grabbed him have changed in colour, thickness, and amount.
Revealing mistake: in the scene when both Freddie's dive off the roller coaster onto an inflatable building, they slide off the building, in the far away shot, they're halfway off the roof to the ground, and the scene cuts to a closer shot as they're sliding to the end of the roof.
Continuity mistake: This error occurs in the scene where Scooby and Cyber Scooby are on the Log Ride, being chased by Jaguaro. The Scoobys have different colored collars on (green and red). Right before Jaguaro reaches them, it can be seen that both Scoobys are wearing red collars, when the "real" Scooby is supposed to wear a green collar. After Jaguaro falls from sight it cuts cut back to the two Scoobys and once again they have different colored collars.
Continuity mistake: When Daphne and Cyber Daphne are in the spooky house. They try to trap Creeper in the trap door, look carefully at the distance of the button,when Daffy presses it, it is right near the trap door. Before that, it was no where near the trap door.
Continuity mistake: At the end level, when the gang are in the arcade, the phantom virus makes one of the videos games grab Fred. Some of the wires are red, but when the wires curl around Freds legs, they are all green.
Continuity mistake: in the final level, where Scooby and Cyber-Scooby are trying to defeat that cat-monster, Scooby has a green collar, while Cyberscoob has a red one. When they push the monster down the log plume, they give each other a high five. In that scene, both Scoobies are wearing red collars.
Factual error: At the beginning, after the blue virus-monster appears, some telephone wires wrap around a scientist's arm. There aren't that many wires in in a normal telephone, nor are they that thick.