According to the game, Mega Man was known as "Mega" prior to becoming the warrior robot Mega Man. This is incorrect; in all other games he was known as "Rock" prior to becoming Mega Man.
While in the original canon Dr Wily stole Proto Man away from Dr Light, here he is seemingly unaware of his existence.
Proto Man states he has an unstable nuclear core. In official canon, he has an unstable SOLAR core.