In the final level of the game 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. When the Jaguar monster goes over the water flume, both Scooby's 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.
Early in the "Hello Cyberdream" montage sequence, the Mystery Inc. gang enters the "Underwater" level in trad-digital animation. The animation style switches to traditional, the style of the first three Scooby-Doo movies, from when Shaggy & Scooby hold their breaths until their quick retrieval of the box of Scooby Snax from the incoming shark. The "Backyard" level reverts the animation style back to trad-digital.
When the Virus makes the telephone attack Eric in the opening, the wires wrap around Eric's wrist. In the flashback, the wires are around his sleeve.
Splicing error: If you slow very down on when the original and cyber versions of the Mystery Inc. gang runaway from the batting cage when they encountered the Phantom Virius, you can see the frame of Shaggy and Scooby-Doo , taken directly from Scooby-Doo and the Alien Invaders (2000), for a split-millisecond.
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", in Daphne's voice.
When Bill said "Look, [the Phantom Virus]' absorbing all our computer data!" at the beginning of the film, he said it in Eric's voice.
During "Double Double Joint", when both Velmas run into the petting zoo, followed by Old Iron Face, it clearly states "CYBER AND PETTING ZOO" on a banner behind them. The "L" in CYBERLAND is missing.