According to STI director Roger Hector, Michael Jackson was initially brought in during development to compose music for the game, even though no mention of his involvement was included in any of the game's credits. This was supposedly due to the scandals that arose around Jackson at the time. His involvement was removed from the title, and much reworking, including all the started music, had to be done.

In December 2009, Michael Jackson's composer Bradley Buxer (credited in Sonic 3 as Brad Buxer) told French magazine Black & White that Jackson was actually involved with some of Sonic 3's compositions, supposedly not being credited because he wasn't happy with how they sounded, due to the lack of optimal sound reproduction on the Genesis.

If you wait roughly 47 minutes on Sonic the Hedgehog 3's file select screen, the music changes. It's not fully known if this is an Easter egg or just a glitch.

The game was meant to be longer, but due to time constraints, the high manufacturing costs of a 34 megabit cartridge with NVRAM, and Sega's commitment to a major McDonald's Happy Meal promotion featuring a sweepstakes to win a copy of the game, the decision was made to split the game into two games, Sonic the Hedgehog 3, and Sonic & Knuckles. Evidence of this split can be found in the level select menu (sound test), where levels from the second game (such as Flying Battery, Mushroom Vally, and Sandopolis) can be found.

Sonic was planned to fall asleep if you wait around, but the sprite wasn't used.

According to an interview with game developer J. Pataki, the "Get Blue Spheres" message at the start of Special Stages originally said "Get Blue Balls". This was changed by the mostly male staff to avoid any sexual undertones.

Fervord records uncovered an unreleased track by "The Jetzons" made around 1984 called "Hard Times", which was found to strongly resemble "Ice Cap Zone" from Sonic the Hedgehog 3. This is likely more than coincidental, seeing as how Brad Buxer was the keyboardist for the Jetzons at the time, and is also credited for working on the soundtrack for Sonic the Hedgehog 3 alongside Michael Jackson.

It's possible to exploit a glitch and destroy Dr. Robotnik before he flees the first time in Launch Base Zone. By hitting Robotnik with Tails 256 times (Sonic and Tails mode) he will pop and a Flicky will fly away. This is easiest done in Debug Mode, but is possible in 1P mode.

Originally, Sonic was going to use a surfboard to get onto Angel Island. This was changed to him flying in as Super Sonic, most likely to connect this game with the true ending of Sonic The Hedgehog 2. The surfboard sprites can still be found in the game's data.

In 1994, London pop group Right Said Fred was hired by Sega of Europe to do a promotional tie-in for the game. Wonderman was released as a single with reworked instrumentals and lyrics to tie into the game. The music video also featured gameplay footage from the game.

Similar to how Sonic the Hedgehog 2's release was on a Tuesday and was dubbed "Sonic 2sday", this game's release in the US was on February 2 - the holiday known as Groundhog Day - and was dubbed "Hedgehog Day".

It's possible to access Flying Battery Zone in Sonic 3 (without Sonic & Knuckles) by using Game Genie Codes.
The stage is extremely glitchy and clearly either isn't finished or is lacking resources from Sonic & Knuckles. Despite this, the Boss fights are functional and the stage can still be finished.

There are unused Routes in most stages of Sonic 3 (without Sonic & Knuckles) that only Knuckles can enter. The unused routes are still be playable, but the Bosses weren't added until Sonic & Knuckles was released with the option to connect the two games together.

Completing a level with 9:59 on the timer will give the player a 100000 Time Bonus.

The ball-shaped planet in the 3D special stage was based on King Kai's Planet from the Dragon Ball anime series.

In the game's North American manual under the "Even More Sonic Super Play Tips" section, the last tip subtly addresses how to deal with glitches resulting from running too fast by branding them as "diabolical traps" set by Dr. Robotnik that "take advantage of Sonic's ultra-fast speed".

In Carnival Night Zone, there is an infamous obstacle known as the "barrel" - a red and white tube that moves up and down depending on what direction is pressed on the control stick, but is animated in a way that makes it appear as if you have to bounce on it to gain momentum - this obstacle has caused a lot of grief to Sonic fans playing the game over the years, and as a result Sonic 3 game designer Takashi Iizuka and lead programmer Yuji Naka officially apologized for the barrel at the Summer of Sonic 2011.

Concept artwork for Sonic the Hedgehog 3 shows that before Knuckles was an echidna, he was conceived as a hedgehog, cat, and eventually mole. During the period in which he was a mole, he was known as "Stealth the Mole", could dig, and had a shovel to attack with. Additionally, a dropped plotline from when Knuckles was a hedgehog revolved around Tails admiring him due to his resemblance to Sonic.

A concept document for Sonic the Hedgehog 3 shows that Knuckles was originally going to be able to walk up walls and ceilings instead of just climbing walls, and break down walls with a whirlwind attack rather than his fists. The McDonald's Happy Meal toy of Knuckles included in their Sonic 3 promotion, which is a wheeled toy that pilots a cloud, may be a leftover of this unused character trait.