The first game has Wily seeking four super programs. Three of which we see him find in the game - Power Plant, Water works, and Lan's oven. They're all actually connected to the scilab. Who's to say that the wood tetra code wasn't in some place connected to the scilab or a scilab employee?
Why would Dr. Hikari keep a super program inside his house of all places? So he could keep an eye on it. What happens when he's not home of course, it gets taken. He would have probably been able to fix the oven himself.
In Network Transmission one stage has ShadowMan.EXE destroying a critical WWW ID rather than allow MegaMan.EXE and Lan to obtain it and infiltrate their network. The reason why Dr. Hikari was able to reassemble the ID was because the file destruction was done too quickly and not thoroughly enough, making the fragments MegaMan retrieved after the fight enough to reconstruct the file by various methods of parity-based data reconstruction.
The "Cyberknobs" and virtual gas in the gas-powered heater right at the start of Battle Network 2 might seem weird, until you realise that they could represent a form of DMA security measure that moves data between memory spaces. Other strange measures that appear to force MegaMan.exe around might represent similar security measures.
Why do you need to get your friend's security codes again each games? Simple: They either changed their passwords, or the security certificates they gave you last game have already expired!
In the third game, the first round of preliminaries for the N1 Grand Prix have you being told simple true or false questions and having to fetch the correstponding "TrueData" or "FalseData" from the net. This actually makes a lot of sense, if you consider this an AI competition the first thing they'd likely do is test whether the entrants' programs return the correct values for simple Boolean expressions. After all, any program that couldn't handle them or gives the wrong value is clearly fundamentally flawed at the most basic level. "If you add the numbers 1 to 10, you get 54. True or False?" actually sounds like pretty typical test data for a program.
So,Mega's DNA program was altered to diffuse his connection to Lan? Well, that incredibly minor change was probably changing his iris color from brown, which Hub presumably had as Lan's twin, to green, which he has as Mega.
Dex has a Porn Stash in the first game. Considering that his computer interface is sentient, hardcopy porn is probably the only way to keep it private.
One particularly unfair phenomenon many players note is that other characters will often simply teleport into the middle of the scene at their own convenience, which Mega can't do. Thing is, this isn't Cutscene Power to the Max — all these characters are capable of Teleport Spamin battle, too!
The game has some Zeerust from the 2000s if one can spot it. Curiously though, you can still jack into things such as televisions that look like CRT sets from the 70s and 80s and Dex still has a CRT monitor for his computer. Why would these old looking devices have a jack-in port? That's the thing - old looking - they were designed to look "Retro" while still containing all the modern conveniences and practicality one would expect today! This isn't unheard of at all in the new tens.
In the first game, Lan has to be physically at the device to jack into it, whereas in the second game he has to have a Wireless Adapter put into the jack in port. Later on, he can do so wirelessly. Funny enough, PET Jack-in technology goes from plug-ins to wireless-with-dongles to what resembles wireless connectivity such as Bluetooth... which happened with a lot of devices over the years (Headphones and radios) and, most importantly... game boy advance and DS-systems. The Game Boy Advance, like its predecessor, required a cable to play with another person. Then came a wireless adapter, then the DS and the 3DS had wireless connectivity built in automatically. Technology Marches On.
The adults' uselessness is glaringly obvious in all of the games, but it makes sense when you remember that Tadashi Hikari, Lan's Grandfather, was the one who invented the modern net as the characters know it. This means that Lan's generation is the only one who grew up completely in the digital age. In the present day real world, the most talented Hackers and Technology experts are the generation who have just come of age, the first true generation that grew up with technology, while the laws and legislature drafted by the older generations are woefully behind in keeping up with it. It's likely that, had these been dealt with normal non-net-based methods, the adults would be considerably more competent.
Lan's grandfather's name, translated into English, is Dr. Right Light, a nod to the old R/L translation issues that Dr. Light's name suffered in the NES era.
The second game's Undernet stands out as abnormal, compared to the rest of the series, being essentially speakers. This seems bizarre, but it makes sense if you're aware of the concept of noise and how it negatively affects data (or just played Star Force 3 for a simpler explanation). What's the best way to keep people out of the know out of your secret area? Make it seem like it's full of noise.
Lan had a bit of an ego in the second and third games, but becomes not only humble and modest, but appeared to lack confidence in later games. This is all part of his character development. After defeating the Life Virus and saving Net Society from Wily in the first game, Lan let the incident go to his head, bragging about it in Network Transmission despite Chaud quickly shooting him down, rightfully (if not harshly) pointing out Lan didn't do it alone. Then in the the third game, Mamoru called him a star for his performance in the N1 Grand Prix and is escalated further when he saved the hospital Mamoru is in from a WWW attack and gets an award ceremony for his heroic deed. As egotistical as it was, it also made Lan confident. Lan has a change in his attitude in the fifth game when he's reluctant to join Team Protoman/Colonel prompting Chaud/Baryl to remind Lan's accomplishments in past games of defeating WWW, Gospel, and Dr. Regal. He also refuses to take over as team leader after the titular navis are kidnapped by Nebula. Why the sudden lack of confidence? Think back to the third game after the hospital hero incident. What was the next chapter? Mr. Match used Lan's brave heroics to manipulate his ego and trick him into installing dangerous software data that endangered many humans and programs, including Dr. Hikari, his dad. That's when Lan changed. He was put in a state of guilt and while he recovered, he learned a lesson (whether or not he knows it) your ego is a weapon people can use to manipulate you into doing their dirty work for them and harm innocent people both real and digital. Lan has still continued to pull heroic deeds but doesn't let them get to his head so as not to accidentally endanger others again.
In the first game during the Ice Man.EXE scenario, Lan mistakenly unleashes bad water into Den City trying to fix the Waterworks system and apparently what ever is in the water is nasty enough to sicken people in minutes if not seconds after drinking! Just what could it be in the water that acts fast enough that Lan watches a guy collapse seconds after drinking said water?
Heck, look at just how stupid the adults are through the series! Eleven-twelve year olds wind up saving the world despite people netbattling for years. The way to get into the main computer for a country can be accessed by children easily. Just how stupid are these people?
Sci Lab hiring a known terrorist like Mr. Match is so ridiculous even Lan doesn't believe him and insists on checking his references, three nondescript "scientist" NPCs scattered throughout the building. If you remember where each one is and talk to them during/after the inevitable firebombing, all three admit to being WWW agents planted specifically to get Match in. How much sabotage could these guys have accomplished beforehand? How many more of these undercover agents have gone unnoticed, and could still be at large?
Lan's father, grandfather, and identical twin all have the same genetic heart condition. It's never actually mentioned, but presumably Lan himself has it, too.
It's possible that the heart condition is actually dual-recessive - and Lan lucked out by having a dominant gene. However, there is still a fair chance that he is a carrier of the gene that causes it, meaning that it's likely to plague his family line unless they marry someone with a dual-dominant allele.
In the first game, the WWW members have their own metroline allowing them to sneak into ACDC, however, the metroline is hidden underneath the school's statue/fountain which is behind the school gate, but when Higsby first arrives, he's standing outside of the school gates.
He arrived earlier and acted as if he arrived via the normal metro to avoid any suspicion.
In BN 4, Higsby is aware that Dark Chips are evil and tells Lan to get rid of it, but in BN 5, a couple of Dark Chips are obtained through the Number Trader.
When fighting PlanetMan his entire field is made of holes (except for the one he's standing on) for his planets to circle around him. However, PlanetMan's Navi Chip requires solid panels for the planets.
In Network Transmission, the Professor unleashes an army of navis on you created from data he had Zero collect. One of those navis is ColorMan even though he wasn't infected by the Zero Virus, hacked by the fake vaccine, or working for the Professor like StarMan.
Colorman wasn't infected before fighting the infected Megaman, you mean.
In the later games, where Lan's PET is wireless and uses infrared rays, why does he still have to be next to a jack-in port if he should be able access it from further away? While outdoor ports can be justified due to sunlight interfering with infrared, there's nothing excusing indoor ports. It's more jarring in the fifth game where a thief can steal a program from outside a room, establishing the effective range of the infrared signals.