While Lan's Net Navi Megaman is incredily powerful, Lan himself is still just an ordinary kid with little fighting skills or experience. You'd Expect: While Lan is currently distracted netbattling against an enemy Navi, the operator just confront him physically and knock him out, taking him to the Big Bad in question while abducting the PET away from him, leaving him completely defenseless. Instead: They never think of doing this until the last segment of the final game when three adults realize they could take on Lan unarmed but by then, they already invented Copybot that allows the Navi to enter the real world. Even worse: Early on in the fifth game, the lab of Lan's father is flooded with sleeping gas, knocking Lan, Dex, Mayl, Yai and Dr. Hikari out cold. Dr. Regal enters the lab, Dr. Hikari is kidnapped and the PETs of Dex, Mayl and Yai are stolen. The only reason Lan's PET is not stolen by the villain is that Lan happened to be on the other side of a divider when he was knocked out by the gas. If Dr. Regal and his mooks had searched the lab a bit more thoroughly, the game would have ended very different.
In 3, during the Hero of ACDC arc, Mr Match approaches Lan and uses peer pressure to trick him into loading in mysterious code "packages" laden with malware that eventually cause a fire in a research laboratory. Mr Match had previously used a series of planted WWW agents and some clever social engineering to bluff Lan into believing that he had genuinely reformed, and preyed on the resulting trust to trick Lan in this fashion. You'd Expect: Lan to check the packages or get someone like his father to vet them before doing anything with them. Instead: He allows Mr Match to play on his ego and manipulate him into playing along, disregarding standard IT security practices, resulting in the endangerment of the lives of the researchers including his father.
The program data packets Mr. Match gives Lan are named "FireData", "HeatData", and "FlamData". Objects with "____Data" names are typically literal cyberspace versions of whatever is in the blank. These data packets are no different; the program NPCs MegaMan delivers them to comment that the packets are very hot to the touch (which surely MegaMan would've noticed) and become painfully overheated immediately upon installing the data into themselves. It should be noted that MegaMan is the more observant and level-headed of the two protagonists. You'd Think: MegaMan would put two and two together and realize the infamous cyberterrorist pyromaniac arsonist is NOT reformed, and is tricking Lan into installing obviously-named data for virtual fire on key Scilab systems so he can set the internet ablaze again. Upon realizing that, he would refuse to cooperate with Lan until he does the above. Instead: Although he does question it a few times, he rolls with it when Lan dismisses the concern and goes on making the deliveries and installing the data as instructed. Cue the game's second instance of the Energy Change Scrappy Mechanic and the player wishing he'd stocked up on more water-element chips to put out virtual fires with. Even Worse: HeatData was a Plot Coupon late in the previous game, so MegaMan has handled it before. The MrProg he got it from even explained as he was handing it over that MrProgs not explicitly specialized to resist HeatData's extreme heat output would overheat and burn up if they tried to install it.
By the final chapter of the same game, it should have been proven beyond any doubt that anything and everything with a computer and a jack-in port can and will be hacked and used to attack those around it by WWW. After a series of incidents caused by WWW operatives, the organization has finally managed to capture Alpha, the Artifact of Doom mentioned throughout the game that will bring about The End of the World as We Know It when they finish bringing it online. The military decides that this has officially escalated things past the Godzilla Threshold, places the real world under martial law, and begins deploying tanks in civilian areas to protect against WWW. You’d Expect: the military to field manned, non-computerized machinery that can’t be hacked and made to attack them or nearby civilians instead of deploying automated robotic war machines originally created by the Big Bad. Instead: they deploy automated robotic war machines originally created by the Big Bad. WWW’s work on Alpha causes the tanks to go haywire and start firing on civilians the same morning they’re deployed.
The entirety of 3's plot runs on idiocy. The WWW is trying to unleash a Sealed Evil in a Can. You’d Expect: that the keys to unseal that can would be kept in tightly secured locations. Or better yet, destroyed entirely so the can could never be unlocked. Instead: the keys are kept in unsecured locations and are basically unguarded by anyone. It is only because the Hero happens to be in the area on that day that the villains face any opposition. Even Worse: Three of the locations are in areas of high civilian traffic. A school, a zoo, and a hospital. Should some radical terrorist group decide to go looking for those keys, a lot of people could be endangered, which is what happens. It is a wonder that anyone in charge of the game's security forces is still employed in the sequels.