Ending Fatigue: The final level of the game takes up the bulk of the movie and mostly consists of the two gangs outwitting the monsters again and again, one by one. There's even a second chase song montage that helps with the final level's severe lack of plot progression, making for a very slow final act.
Ensemble Darkhorse: The Phantom Virus himself is insanely popular among the Scooby-Doo fandom.
Fridge Brilliance: The Cyber Gang don't seem to care about going back to level 1, implying they'll be unchanged by the game resetting (which is confirmed the next time the game is started), but the Phantom Virus is deleted when they win and the game resets. Why? The Cyber Gang are programmed into the game and thus part of its code, and the Phantom Virus is a foreign entity, meaning the game doesn't know it needs to recreate him on Level 1.
Another more thought-provoking example that's doubles as a Mythology Gag; in the original Jaguaro episode, the costume of it is pretty big compared to Shaggy and Scooby, and it makes a weird howl. However, when the others find the statue, it's about the same size as them. If we assume Eric based his research for the game's cyber-Jaguaro off the internet, it's no doubt based upon the mythology and the statue, and not Barney's costume, hence why it's size appropriate and growls like a cat and not whatever the hell it sounded like in the original episode.
Fridge Logic: The magnet Shaggy brings into the game doesn't affect anything until he pulls it out and holds it close to the Cyber Gang, and it only affects the Cyber Gang and the Virus, not the game's environment. Not to mention the magnet would be made up of pixels just like the Cyber Gang and shouldn't affect them like that.
In this movie the gang have a scene where they comment on the cyber-gang's outdated attire. In the very next movie, the gang return to their classic looks.
Idiot Plot: Arguably. As Caddicarus points out, the virus keeps making mistakes and leaves clues of it's creator everywhere, yet it must have been programmed to do so. When the gang starts to connect the dots, Bill ruins his cover by attempting to run away, which leads to his capture. While the first part could be explained with the virus going rogue, his escape attempt amounts to little else than an Idiot Ball.
Moral Event Horizon: Bill's creation of the Phantom Virus to scare off Eric would just be normal pettiness were it not for the Nightmare Fuel below, but then he intentionally beams the Mystery Gang into Eric's game - where they, for all intents and purposes, could've been maimed, melted, eaten, and otherwise killed numerous times. The story doesn't explore the implications, but it's essentially an attempt at assisted murder with no recoverable evidence.