A topic onGameFAQs shows quite a few people didn't realize that Wizard is a pun on the type of program.
There's another case of this in the first game: it seems that Andromeda is a stupid name for a world-destroying war machine, until you realize that the FM-King's name, Cepheus, is also that of the mythological Andromeda's father, both of whom also are constellations in the sky to fit in with the theme.
The term "Brother" seems like a rather odd term to use to describe relationships with other people regardless of gender, but then you find out in the second game that Lan Hikari started the system, and he based it off his bond with Hub. You see, he notices that whenever he and Hub worked together, miracles could happen due to this "Link Power", and decided to try and connect the world through this. He succeeded, to say the least. Also, 'brother' sounds like 'broader'. So 'brotherband' can be read as 'broader band', a pun on broadband.
Gemini Spark, Crown Thunder, and Hollow are all the most powerful fighters in their own class? Why? They're Elec-Type, which means that their powers are the closest to electromagnetism proper, where as all the other powers are modified into the elements.
Fridge Logic: Many moments from the first game become borderline illogical when you think about it. Wouldn't putting a car in the way of the truck have caused severe injuries? Was Sonia contractually obligated to give that concert, or not? (If she was, she could have been sued for damages. If not, she could have sued her manager. This may be a case of No Such Thing As Lawyers...) Why didn't the principal just make Mr. Shepar a Social Studies teacher? (Or barring that, that one teacher who teaches that nebulous class known as "Health", or even just Homeroom?)
They justify the bit about the car when Geo wonders if everyone's okay. Turns out they all got sucked into the computer system of the truck.
Also, the problem with Mr. Shepar's class (he does indeed teach homeroom - it's just all day with his one class) is that he's the one teacher at school who doesn't use the StudyWave as per the principal's desire; the principal gets fed up and blackmails him into needing to find a job to sustain himself and 7 kids.
Regarding the anime, can someone please explain how Battle Cards were originally supposed to be used? All that's seen is Geo swiping a few sword cards and some viruses getting sliced, but how did other cards come to be and how the heck are other people supposed to use them?
It's supposed to be played as a trading card game. At Big Wave store they even have a table to play it. As strange it may seem, it is a trading card game based on viruses!
Some early statements in the first game suggest that when the viruses started showing up, Battle Cards were developed and released to the public, likely to be used by Navis as Battle Chips had been. Since most people have Transers and at least one Navi, this makes sense. That aside, perhaps Net Battling and Battle Chips simply went underground after a while? 200 years is a long time...
More Fridge Logic: All the characters in Star Force 2'sBonus Dungeon all behave as though Mega Man carries the OOPArt, even though it was ripped from his body and fell into the sea during the events of the main game itself.