In the Game Boy Color enhanced releases of the game, while still possible to play the game on a Game Boy or a Game Boy Color, the save files for both systems were not compatible with each other. For this reason, when trying to play a Game Boy Color save file on a Game Boy (or vice versa) the game will go through a set of menus to delete the old save data to accommodate that of the other system.

A penguin enemy in the English version throws bowling balls at Wario. If they hit, he becomes dizzy, burps, and needs to splash himself off with water to go back to normal. In the Japanese version, the penguin actually throws pints of beer. This explains the out of place animations and why Wario needs water. The beer was censored for obvious reasons.