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.
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.
In this movie the gang have a scene where they comment on the cyber-gang's outdated attire.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.
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 they intentionally beam the Mystery Gang into Eric's game - where they, for all intents and purposes, could've been maimed, melted, eaten, and otherwise numerous times. The story doesn't explore the implications, but it's essentially an attempt at assisted murder with no recoverable evidence.