Christmas Rushed: This was such an ambitious game, that it became clear that it would be impossible to finish it as a whole in time, forcing Sega to split the entire game in half, and even then Sonic 3 arrived later than expected (February 1994), with Sonic & Knuckles arriving eight months later with its Lock-On Technology added to allow Sonic 3 to be played as it was originally planned. It didn't help that McDonald's, who had a tie-in deal with the game, ended up pushing Happy Meal toys before the game was released, forcing Sega's hand in the entire thing. On top of that, both games are loaded of glitches and polish issues, some of which are game breaking, to the point where the manual had to handwave these issues (such as Sonic being liable to accidentally get stuck in certain scenery or Tails sometimes being unable to complete Hydrocity in standalone Sonic 3 due to the screen locking up) as "diabolical traps" set up by Robotnik.
Copy Protection: Pirate copies of the cartridge obviously do not have the lock-on slot. This means a huge chunk of content will be unavailable, so even though the game is still fully playable, it's a lot less interesting.
Game Mod: Sonic 3 Complete is a mod that polishes the game in areas that the official Sonic 3 & Knuckles neglected (fixing glitches, giving Super Sonic actual sprites for certain level gimmicks) as well as allowing a plethora of options such as choosing individual tracks between Sonic 3 or Sonic & Knuckles and allowing the ability to play Sonic 3 or Sonic & Knuckles standalone in the same game. It also added some goodies like restoring the "Beta" level order (Flying Battery after Carnival Night), and the option to do the Super Peel Out from Sonic CD. For more extras, you can even create IPS patches that change the game even further, such as changing Sonic back to his Sonic 1 and Sonic 2 sprites, with new sprites to accommodate them for all of the actions he could only do in Sonic 3 & Knuckles.
God Never Said That: Takashi Iizuka only said that Super Emeralds were a late addition to Sonic 3 & Knuckles due to wanting a bonus lock-on incentive, which causes certain fans to interpret them as being "non-canon".
Manual Misprint: The two Badniks from Flying Battery Zone in Sonic & Knuckles first showed up in the Sonic 3 instruction manual (though it's understandable given Flying Battery's last-minute removal from 3).
Refitted for Sequel: Sonic & Knuckles consists almost entirely of material that was originally intended for Sonic 3 but was cut due to time and hardware constraints. The two games can, however, be locked on together, which creates the official full game, and the longest in the original Sonic trilogy.
According to Cirocco Jones (mistakenly credited as Scirocco in the Sonic 3 credits), there's a huge legal mess concerning the music used in the games, likely due to unpaid royalties, improperly crediting the musicians, or (as was the case with Dreams Come True), licensing issues. Considering that two of the music composers (Michael Jackson and Brad Buxer) directly sampled songs from their respective discographies, the latter is the most likely. It's generally believed this is the reason why a Taxman/Stealth remaster like the first two Genesis games is unlikely (though Taxman made a proof of concept video in honor of the game's 20th anniversary), as Sega has only been able to release direct emulations of the original game or recoded versions with different music (as seen in the PC version).
The music issues are likely the reason why the incredibly popular IceCap Zone hasn't appeared in Generations nor Mania, despite both games being dedicated to re-imagining popular levels from previous games. Its background music was an originally unreleased song called "Hard Times" by The Jetzons, a band that composer Brad Buxer was once a part of. Because of this, Sega likely does not hold the rights to the song, preventing its appearance in said games. Said legalese is the reason Sonic 3 and Sonic & Knuckles are omitted from the Sega Genesis Classics compilation for the PlayStation 4 and Xbox One.
in February 2018, Naoto Ohshima revealed that Michael Jackson sent Sonic Team a demo tape of original songs for the game. According to Ohshima, none of the songs from the tape were used, and Sega has the tape locked away in a vault. Whether or not any of those songs became the one of the MJ-made tracks in Sonic 3 will likely never be known.
Shrug of God: The Super Emeralds only existed in this game and they simply vanished after the events of the game:note In Sonic Mania, stone relics carved in the likeness of the Super Emeralds appear in their place at the Hidden Palace.
Kazuyuki Hoshino: "They're gone. I don't know how it happened, but they're gone."
Troubled Production: Sonic the Hedgehog 3 and Sonic & Knuckles were once planned to be one big game, just the basic Sonic the Hedgehog 3. However, time restraints forced Sega to split the game in two in time for 3's release, leaving many fans to wonder what these other stages were once they put in the insanely difficult Stage Select code. When Sonic & Knuckles was being made, the initial plan was that it could hook up to Sonic the Hedgehog, Sonic the Hedgehog 2 and Sonic the Hedgehog 3 for new playing adventures. However, complications with the code in Sonic the Hedgehog forced them to scrap it and replace it with the Blue Spheres mini game collection. It was initially said that Knuckles gliding onto a treadmill in Scrap Brain Zone caused the game to crash. However, it was revealed later on that it was because most of the game's graphics was built around Sonic's color palette, and introducing Knuckles would end up changing every other graphic in the game. A fan did a hack years later by reducing Knuckles' color scheme to match the games' limited palette. Due to the introduction of Super Sonic in Sonic the Hedgehog 2, that game did not suffer such problems.
And then Michael Jackson's rumored involvement in the game's music is a whole story of its own, which ranges from anonymous credits and dropped finished tracks because of his child molestation allegations, to him being dissatisfied with the Genesis sound hardware.
According to the PixN'Love History of Sonic the Hedgehog book, the "Time Restraints" problem turned out to be a business deal with McDonald's — McDonald's had set up a deal for Sonic 3-related Happy Meal toys, expecting a Christmas release. However, when that didn't happen, Sega was forced to rush Sonic 3 out with just the six stages. With as big as Sonic 3 was, stage-wise, it wasn't too bad of a strike.
There tends to be confusion as to why Sonic 1 could not be locked in with Sonic & Knuckles. The two most popular explanations are that Knuckles would have dramatically altered the color pallete or that Knuckles gliding on conveyor belts in Scrap Brain Zone would cause the game to crash. Both of which were solved by the famous ROM hack Knuckles the Echidna in Sonic the Hedgehog as well as any future ROM hacks starring characters other than Sonic.
Despite what your friends (and basic logic) told you, it's not possible to beat Fire Breath the first time you see it and stop it from burning Angel Island. No matter how fast you hit it, it'll successfully set off the firebombs and escape with its robotic life.
Sega Magazine (UK) claimed in its issue 11 (page 70) that there was a secret character hidden in Sonic & Knuckles: "Rankles, the green otter with outsize sparkly ankles and Knuckles' sidekick." They offered a million pounds to the first person to send them a photo of Rankles. At the end of the paragraph, they outright admitted that they just made him up, but some kids at the time missed the addendum and thought it was all real:note As an extra bit of irony, there actually is a glitchy green palette swap of Knuckles, who looks an awful lot like the magazine's illustration of "Rankles"... But he's in the Sonic 3 cartridge, not in Sonic & Knuckles.
Anyone who sees Rankles should call Alcoholics Anonymous because Tom Guise just made him up. And we're afraid we couldn't give you the million pounds anyway.
This game has an item monitor that can only be accessed through debug mode. The item in question is just a blue "S" that grants the character their super form and 50 rings, even if the player did not collect all the Chaos Emeralds. Whether the item was just for bug/balance testing or something more remains to be seen.
The magazine Sega Magazin makes mention of a "Help item". Sonic would break a monitor and whistle for Tails who would then carry him about akin to a second player. Although not present in the final game, Sonic's whistling animation is still present within the game's code and a whistling sound is heard at the start of Doomsday Zone.
Flying Battery Zone was originally planned to be in the Sonic 3 half, between Carnival Night and IceCap.note Sonic would have improvised the broken door as a snowboard, as demonstrated in Sonic 3 Complete. Time constraints intervened, and it (along with at least "Mushroom Valley" and Sandopolis) had to be cut and moved to the Sonic & Knuckles half. In the end, this was probably a good call, as it helps to balance the emerald collection in the combined game.note However, the snowboarding off a sheet of metal from Flying Battery Zone at the beginning of IceCap did inspire the opening to the Hero side story as well as the first part of the City Escape level in Sonic Adventure 2 a few years later with something similar to the original snowboarding planned transition between Flying Battery and IceCap from this game happening in it.
In a case of What Could Not Have Been, the Super Emeralds and their powers were not part of the original plan. According to Takashi Iizuka at Sonic Boom 2013, they were only added after the game was split so the player would have an incentive to go through another set of Special Stages.
A theoretical Knuckles the Echidna in Sonic the Hedgehog was going to be accessible by locking the game to Sonic 1. However, this idea was scrapped, mostly due to palette issues (as all the in-game graphics used Sonic's palette as a base) and bugs involving the gliding mechanic in Scrap Brain Zone (though there have been many ROM hacks since then that fix both of these issues).
Sonic 3 was intended to have both Tails and Knuckles as playable characters but, after being rushed for time, only Tails was left in the game planning. You can play as Knuckles when the S3 cartridge is locked onto the S&K cartridge, however.
Sonic & Knuckles and Sonic 3 w/ Lock On Technology were intended to be a single large game, code named Project Blue Red in alpha and beta stages, Sega realized that the cost of producing this one game (which would need to be larger then their own self-set system cartridge limits allowed) would out weight the cost of splitting it down and making two games which could be linked together.