It is actually possible to "kill" Doctor Wily in the penultimate boss battle with him. After destroying Wily Machine No. 4, switch to Toad Man's "Rain Flush" weapon and fire it so that the screen-clearing rain comes down before Wily leaves the screen in his escape pod. The attack will destroy him with a sound effect and explosion graphic the same as if you were destroying a common stage enemy. Mega Man will now be stuck on this screen forever, as the game does not move on to the next level if you do this.

In Japan, there was a contest to make the 8 Robot Masters that appear in the game. The 8 winners would get a gold cartridge of the game. The carts now go for ¥628,000 (around $8,000) each.

In the credits, three of the Robot Masters have switched numbers despite being placed where they would be if the numbers were correct. Toad Man's should be NO. 26 but it is labeled as NO. 29 which is Ring Man's number, Ring Man is labeled NO. 28 which is Pharaoh Man's number, and Pharaoh Man is labeled as NO. 26 which is Toad Man's number.

There was originally going to be a Sphinx themed mini-boss in Pharaoh Man's stage. It was functional in some demo versions of the game, but the Sphinx is not present in the final release.