Despite most of Sonic CD's soundtrack being replaced for the game's American release, all of the past versions of the level themes remain unchanged from the Japanese/European originals. This is because unlike the rest of the game's soundtrack, in which each song is encoded in the Mixed Mode Compact Disc Digital Audio format (more commonly known as Redbook audio), the "past" themes are encoded using pulse-code modulation, making them much harder to switch out.

Originally, the Special Stages were going to have Sonic navigate a rotating maze, building upon the framework of Sonic 1's Special Stage. Although similar, Sonic CD's Special Stage was planned to have two rotating layers that the player switched between.

According to BEEP and Marukatsu MegaDrive magazine interviews, with game's planner Hiroaki Chino, the developers thought the Special Stage was very slow, so they decided to redo it to make better use of the Sega CD hardware.

This special stage concept would eventually be used in Sonic Superstars.

Game's landscape designer Masato Nishimura stated on Twitter, that Wacky Workbench was originally called 'Crazy Toy Box'. The reason for this change was unknown.

In a 1993 interview with the game's planner Hiroaki Chino in issue no. 7 of Marukatsu Mega Drive, he was asked what the biggest changes were in Sonic CD compared to past games that were released on cartridges? He responded: