Bug: After finishing the game numerous times, the game might start to show glitches like enemies walking in thin air or wandering off the map.
Continuity mistake: In the intro at the very start of the game, it shows Shade being played in Mystic Ruins. However, this isn't possible in the actual gameplay as you can only play Shade after the Metropolis zone, and by this point you can't go back to Mystic Ruins.
Trivia: Near the end of the game, as the everyone is escaping into their ship, no one is seen carrying the Master Emerald.