In both Mega Man 5 and Mega Man 10, Dr. Wily is able to get his technology to Dr. Light's lab, with Dark Man kidnapping Dr. Light in 5 and flying his saucer right into Mega Man's hands in 10. You'd expect he exploit this ability to kill he enemies before his attacks. Either shoot Light or remote pilot a bomb into Mega Man. Instead: he uses this to divert blame and launches his normal attack. Both times. By this point it's his own fault Mega Man kicks his ass.
In Mega Man 9, Wily claims Light is sick and brings Mega Man over to him. Proto Man teleports in and tells Mega Man that Wily is lying. You'd expect: Mega Man would realize that 6 of the last 9 games (including this one) involved Wily manipulating things behind the scenes. Instead He believes Wily and almost dies when Wily cheap shots him. Even Worse Proto Man didn't believe Wily, and yet, rather than cover his naive brother in case Wily tried something, he teleported out. However: It's possible he was trying to let Mega Man learn the lesson through the school of hard knocks. He probably followed it up with an I Told You So or something after the events of the game, because frankly, Mega Man kind of deserved it.
Also in 9, Dr. Wily, the notorious criminal, terrorist, and Mad Scientist, appears on global TV and declares that Dr. Light is actually the evil one, not himself. But, if the entire planet will funnel their money into Wily's Swiss Bank Account, he will personally bring Dr. Light to justice. You'd expect: The entire planet, or at least the governments and police forces, to tell Wily to screw off, because they know that he's the one responsible for the last eight or nine attempts to take over the world. Instead: The world buys it like idiots and Dr. Light is arrested.
In Mega Man 6, Dr. Wily is finally arrested. You'd expect: The government to execute him (or at the very least throw him into the highest level security prison they can) since he's tried six times to conquer the world. Add in the Gameboy and various other games up to this point and the number is closer to twenty. Maybe even check his leftover castles, since they didn't blow up this time, to track down his remaining hideouts and robots. Instead: He's kept alive and imprisoned in the middle of the city it seems and do nothing else. It doesn't take long for his back up robots to find him once they activate. Plus, by the looks of things at the end of 6, it looks to be an ordinary jail cell for probably the most dangerous man on the planet.
In Mega Man 7, while Robot Museum was an awesome Nostalgia Level, when you stop and think about it someone really dropped the ball on this one. You'd expect: This is (at least) 46 dangerous, weaponized Robot Masters, they should be destroyed, or at least, locked away in a safe and secure facility where Dr. Wily, or anyone else for that matter, can't get to them. Instead: They put every one of these dangerous robots on display in a Robot Museum, lined up one after the other in what looks like easily breakable glass cases. Its no surprise that Dr. Wily raids the place, its a regular smorgasbord of deadly Robot Masters! The world was just lucky Dr. Wily only managed to run off with three Robot Masters before Mega Man rushed in to chase him out. Even Worse: While we don't know the actual state of the displayed robots, they obviously had enough of their original components intact that Dr. Wily was able to pretty easily reactivate Gutsman. So not only did they put the Robot Masters on display, they did not even bother to decommission them properly first! Additionally: The canon is that Robot Masters are restored and made good again between games, and that Wily can copy Robot Masters. Those robots in the museum are copies of the originals. The people in this series actually put functional copies, all as powerful as the originals, in that museum.