I know two, but aren't especifically from Nintendo...
1.- Miyamoto often had nightmares regarding glitches in The Legend of Zelda.
2.- When finished the development for Ocarina of Time, they started creating an expansion for it (Don't remember the name). One of the developers didn't agree with this direction, and Miyamoto challenged him to create a Zelda game within a year in order to scratch this expansion project. Thus here was born Majora's Mask.







