The SEGA Saturn version of the game has a different theme for Tengu Man than in the Playstation version of the game.

In the Saturn version, Cut Man and Wood Man from Mega Man and Mega Man 2 make appearances as mini-bosses in Duo's mini-stage and Search Man's stage respectively. The former is optional, while the latter is mandatory. A remix of their themes also plays while battling them.

Bass's name is mispronounced throughout the game. In the game, his name is pronounced "bass" (like the fish), however his name is meant to be read as "base," since his and Treble's names come from the bass and treble clefs. This has lead to much confusion on how to pronounce his name.