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:

The 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.

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.

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.

In the Sonic Gems Collection version of Sonic CD, the water in the game is clear. That is because it's a direct port of the PC version, which utilized a specific graphics card for the water which wasn't emulated.

Sonic CD's JP/EU intro song "You Can Do Anything/Toot Toot Sonic Warrior" is actually a remix of the theme of Green Hill Zone from the Game Gear/Master System version of Sonic the Hedgehog 2.

The original Sonic CD intro is shorter and slower than in the updated versions. That includes collections and the HD version. The original includes scene of Eggman's face on the mountains in the original, but was cut on the updated versions.

When the code FM40 PCM12 DA11 is inputted in the unlocked sound test menu, a screen with Tails next to a car saying "See you next game!" will appear.

The game's CD also serves as its soundtrack - inserting it into a normal CD player plays the game's music.

There's an extra special stage that can be accessed through the sound test menu by setting all the 3 selections to 07. According to a former Sega Europe QA Tester, an extra Time Stone was to be collectible here. When collected in addition to the previous Time Stones, "S" TV monitors would appear where the ring TVs were previously located. When broken, Sonic would morph into a lesser version of Super Sonic, which would simply grant invincibility and greater speed. Graphics would not change.

The Japanese/European soundtrack for the game is different compared to the American version. An example of this would be the intro and ending songs. In the Japanese version, the intro song is "You Can Do Anything" while the ending song is "Believe In Yourself" by Cosmic Eternity. In the American version, both the intro and ending songs are "Sonic Boom" by Pastiche. Because the American version got a new soundtrack and the intro and ending FMV sequences were being re-edited to fit in time with the respective music, the game was delayed a few months.

In the Japanese manual for Sonic CD, Amy Rose is referred to as "Rosie the Rascal". In the U.S. Manual, her name is listed as Princess Sally. Fans have speculated that her name was changed to Princess Sally in the U.S. manual of Sonic CD to tie the game to the Archie Comics, or the Saturday morning cartoon. All references to Sally were removed in later re-releases of the game.

When Sonic CD was being remade using Christian Whitehead's self-made engine, he wanted to include a new level called "Desert Dazzle". However, SEGA thought it was a bad idea to deviate from the original project. You can actually find a concept image with Christian's initials on it in the sound test by entering PCM:32|DA:8

If the player enters the sound test mode and sets the toggles to FM NO.46, PCM NO.12, and DA NO.25, the game will cut to a screen depicting a collage of Sonics with bizarre, humanlike faces with the boss theme playing over it. Atop the collage is Japanese text which translates to "Infinite fun. Sega Enterprises. –Mazin Picture", referencing a tagline used by the Sega Sougou series of catalogs. Meanwhile, "Mazin" is the childhood nickname of Masato Nishimura, the game's landscape designer; the moniker can also be romanized "Majin", but Nishimura stated on Twitter that he prefers the "Mazin" spelling. According to Nishimura, this Easter egg was planned to have an additional feature where pressing a button combination would change the text to read "Infinite hatred proceeds from excessive fun," a play on the Japanese aphorism "The greatest hate proceeds from the greatest love." However, after unsuccessfully attempting to enter it in the finished game, he theorized that he either forgot the combination or removed it prior to release.

Following the Easter egg's publicizing online, it became a widespread subject of attention for its apparently disturbing nature due to a mixture of its appearance, the eerie tone of the US version's boss theme, and misinterpretations of the "Majin" spelling of Nishimura's nickname as the homophonous 魔人, meaning "demon." This then morphed into a rumor that the Easter egg was designed as an anti-piracy feature, a claim which Sega repeated on the 2011 remaster's Google Play Store listing. However, Nishimura denied that the screen was intended to scare players.

Sonic CD was originally going to be a CD enhanced version of Sonic 2, but after Sonic 2's release, it evolved into its own title. It was also titled "Super Sonic" early in development.

Standing still for 3 minutes will cause Sonic to jump off screen, saying "I'm outta here!" and cause an instant game over, regardless of how many lives you may have.

All level titles in Sonic CD are alliterations.

In Sonic CD, a DJ scene and a Batman tribute image can be brought up in the game sound test area by entering the following codes respectively:

FM NO.42 PCM NO.03 DA NO.01
FM NO.42 PCM NO.04 DA NO.21