When the network canceled the show, the writers dubbed Megabyte's fighter ships "ABCs" and inserted the line "The ABCs - they've turned on us. The treacherous dogs!" in the finale.
Though ABC canceled the series after two seasons, Mainframe produced a third season (and eventually some TV movies) for Canada which eventually aired on cable in the United States. Without ABC to insist upon stories suitable for young children, the episodes took on darker tones.
The end of Season Three features a musical summary of the events of that season. It is done to the tune of "Modern Major General' by Gilbert and Sullivan, from "The Pirates of Penzance"
The code the character Phong uses to unlock the Mainframe Principle Office's secrets throughout the series is "YADDAYADDAYADDA!" In the third season, this code is seen partially written out in binary on a machine of Megabyte's.
Feather McGraw who made five cameo appearances in the series, is never given a name on screen. But is clearly the same Feathers McGraw from "The Wrong Trousers".
There were plans for the fourth season to include 12 episodes broken into three films, along with a 13th musical-special episode, but the final five episodes were never produced.
During pre-production of the series, all the characters were going to be binomes. However animators have successfully achieved in creating a handful of human-like character for the series. The models of the binomes were really easy to change and alter to end up creating a whole cast of extras for the cartoon. As the series progress, more human like characters were introduce than in the first season.
Originally there was going to be a spin-off learning series with the binomes as the character. It never went into production, however a concept art sheet can be seen in the Reboot Art Book.
When BS&P was involved with Seasons 1-2, the writers had to follow a lot of their guidelines on what they can't show on their cartoon. Such rules like forbidding the game or word "hockey", nothing too sexual or violent was to be presented, and the word "wuss" was taboo during certain occasions.
On May 30, 2008; a 2 part web-comic made by "Zeros 2 Heroes" was posted online which contains a story on what happen after the events of "Crouching Binome, Hidden Virus". Even though the comic had a better conclusion than the TV series, a lot of fans wished it was longer and had a better ending.