When Rock sits down to breakfast, Light explains that he can eat, and taste food, and feels hunger, but doesn't need to eat. Yes. He doesn't need to eat, but still gets hungry. Try not to think about that too hard.
When Mega Man captures Wily, he states that the doctor could have used his talents for good. Even though Wily had been doing that for years and not getting credit, which was what led to this whole problem in the first place.
He probably meant something along the lines of, "You could've made your own robots to make money/get recognition legally instead of, you know, trying to take over the world."
How did Mega Man catch wind of that "you're just a useless toy" speech Wily gave? Or was that jab at the end just a coincidence?
How did Wily's floating death castle slip under everyone's radar until it ripped itself out of the ground and started blowing shit up? You'd think someone would notice a damn skull with a "W" on it!
For the same reason no one in the games notices it.
Why was the "mobile fortress for rescuing people" armed with shield generators, cannons, and lasers?
Also: Dr. Light not only leaving military projects around in one convenient location, but keeping them stocked with ammo and power just in case someone wanted to use them again, even after deciding he and Wily wouldn't pursue military contracts anymore.
