Mario being the referee was added at the last minute. While Nintendo owned Punch-Out and there was no legal issue, apparently the creators forgot to ask their bosses permission to put the plumber in the game.
Ten thousand Japanese fans who submitted high scores to a golf game were given gold colored cartridges with Punch-Out. Though Super Macho Man was the final boss, not Mike Tyson.
In later versions of Punch-Out on NES, Mike Tyson is cosmetically replaced by a boxer named Mr. Dream. Most assumed it was Nintendo distancing themselves from his criminal history, but it was because he lost his championship title.
Several passwords for Metal Gear on NES contain clever not so hidden profanity. This triggered Nintendo of America to impose taking vowels out of future passwords.
Shigeru Miyamoto did call the second Zelda game as the least favorite game he helped create.