The American localization prototype of Mega Man 3 showcases the development of the game as it underwent the English translation process, and is a bit glitchier than the final as a result.
The Bolton and Nutton enemies don't blink when they are being put together, much like in the Japanese version.
Much like in the Japanese version, as soon as Mega Man lands on one of the areas of Top Man's Stage, a Bolton and Nutton appears. In the final, Mega Man needs to be at the edge of the platform he's standing on for it to appear.
Proto
Every time a Robot Master is defeated in the prototype, Mega Man gets stuck in his attacking position until the Robot Master's explosion sprites are completely off-screen.
Proto
Final
When Mega Man performs the Top Spin, part of his helmet turns dark blue instead of gray.
When Mega Man lands in the room where he battles Break Man in Magnet Man's, Hard Man's, or Shadow Man's stage, he gets stuck in his "running start" position.
Sometimes, if you lose a life while fighting a boss, the "sweat" particles from Mega Man's attacked sprite will appear after he teleports back into the stage.
Sometimes, if too many objects appear on-screen, they will glitch or other sprites will appear for a split-second.
Mega Man gets stuck in his running animation while Break Man shows up in Gemini Man's stage.
While taking damage, Mega Man may suddenly become invisible and get stuck. After about a minute, the screen will start to scroll to the left until it stops at the beginning of the stage.
Defeating the Doc Robot that has Bubble Man's abilities with Rush Marine in the prototype will cause Mega Man's sprite to glitch.
After Mega Man destroys Shadow Man using Top Spin, not only does he get stuck, but his sprite also gets glitched until the Robot Master's explosion sprites are off-screen.
One of the areas cause the sprites to flicker and change color. They also slow down the framerate of the game. Going down to the next area makes the level retain its original colors and Mega Man and Rush's faces turn purple.