Expectedly, there are multiple leftover graphical elements of the original Puyo Puyo game inside the game's memory (note: the sprite's original palettes from Puyo Puyo are used since the modified game does not feature matching ones):
The cutscene sprites of the player character, Arle Nadja are mostly intact. They are still loaded with the cutscene unmodified, suggesting there were no plans in production stages for Sonic or any other player character to be utilised in Dr Robotnik's Mean Bean Machine.
The full tile set for the Lesson Mode arena is still inside the game (parts being utilised for the background of the Options screen and the Checksum Error message above). Curiously Lesson Mode itself does not load the area, implying it underwent some modification before being omitted altogether.
Some leftover tiles from the original high score screen.
The Lesson stages from Puyo Puyo were not cut from the game and can be accessed by using PAR code 00BEFE:000? (? can be changed to 0-2). The tutorial text is glitchy and no music plays. Coconuts stands in strange positions in the stage cutscenes. Defeating the third Lesson stage advances the player to the ending cutscene.
If playing the game on a Japanese Mega Drive via patch code a sound test will be available in the Options screen. The Game Genie code ADTT-AAAE will also make it appear but will trigger a checksum error if it is enabled before the Sega logo screen.
Some of the songs in the sound test (specifically, 01, 0C, 0D, 0F, 10, 14, and 15) are hidden if the console region is set back to US. However, if the console region is still set to Japan, these tracks will get shown after the normally accessible tracks.
There are a few unused sound effects (mostly leftover from Puyo Puyo) and can be heard in the sound test.
Puyo Puyo's checksum Error still exists in the game, and is triggered the same way.