* ChristmasRushed: The game in its completed state was too ambitious for it to be released as a whole in such a short time. Additionally, UsefulNotes/McDonalds ended up pushing Happy Meal toys before the game was released, which further forced Creator/{{Sega}}'s hand. ''Sonic 3'' was released in February 1994, while ''Sonic & Knuckles'' was released eight months later.
* CopyProtection: 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.
* GameMod: ''[[http://www.s3complete.org/ 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 ''[[VideoGame/SonicTheHedgehogCD Sonic CD]]''. For more extras, you can even create IPS patches that change the game even further, such as changing Sonic back to his ''[[VideoGame/SonicTheHedgehog1 Sonic 1]]'' and ''[[VideoGame/SonicTheHedgehog2 Sonic 2]]'' sprites, with new sprites to accommodate them for all of the actions he could only do in ''Sonic 3 & Knuckles''.
* GodNeverSaidThat: 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 "[[CanonDiscontinuity non-canon]]".
* ManualMisprint: The two Badniks from Flying Battery Zone in ''Sonic & Knuckles'' first showed up in the ''Sonic 3'' instruction manual.
* NamesTheSame:
** In English materials - Blastoid from [[http://info.sonicretro.org/Blastoid Hydrocity]] and [[http://info.sonicretro.org/Sparkle Carnival Night]], and Mushmeanie from [[http://info.sonicretro.org/Mushmeanie Mushroom Hill]] and [[http://info.sonicretro.org/Iwamodoki Lava Reef.]] In Japanese materials, these enemies have separate names, but [[http://info.sonicretro.org/Sandworm Sandworm]] shares its name with the first [[http://info.sonicretro.org/Caterkiller Caterkiller]] from ''VideoGame/{{Sonic the Hedgehog|1}}'' (Gnarl).
** The robotic duplicate of Sonic that appears late in the game also has multiple names depending on the source - Metal Sonic according to the [[AllThereInTheManual back of the original North American release box]] of ''Sonic & Knuckles'', Mecha Sonic according to [[NoExportForYou Japanese strategy guides]], [[Comicbook/ArchieComicsSonicTheHedgehog Archie Comics]], ''VideoGame/LegoDimensions'' and recaps on the ''[[VideoGame/SonicTheHedgehog4 Sonic 4: Episode I]]'' websites, and the Evil Sonic according to the ''ComicBook/SonicTheComic'' Q Zone. Officially, the recurring Metal Sonic from ''Sonic CD'' has no connection with this character, but it MAY be related to the Mecha Sonic robot(s) from either version of ''Sonic 2''.
* ScrewedByTheLawyers:
** 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 (Music/MichaelJackson 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 [[https://www.youtube.com/watch?v=Ct1cErthI6s 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 Ice Cap Zone hasn't appeared in ''[[VideoGame/SonicGenerations Generations]]'' nor ''[[VideoGame/SonicMania 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.
* ShrugOfGod: The Super Emeralds only existed in this game and they simply [[http://www.gameinformer.com/b/features/archive/2017/06/10/more-burning-questions-about-the-sonic-the-hedgehog-franchise-answered.aspx vanished]] after the events of the game:[[note]]In ''VideoGame/SonicMania'', [[spoiler:stone relics carved in the likeness of the Super Emeralds appear in their place at the Hidden Palace.]][[/note]]
-->'''Kazuyuki Hoshino:''' "They're gone. I don't know how it happened, but they're gone."
* UncreditedRole: Music/MichaelJackson contributed to the soundtrack, but he was dissatisfied with the sound capabilities of the UsefulNotes/SegaGenesis and decided to go uncredited.
* UrbanLegendOfZelda:
** 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 [[GameBreakingBug 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 [[http://info.sonicretro.org/Sonic_%26_Knuckles_magazine_articles 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.
-->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.
::: As an extra bit of irony, there actually is [[TheMissingno 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''.
* WhatCouldHaveBeen:
** 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 ''[[GameMod Sonic 3 Complete]]''.[[/note]] 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 ''VideoGame/SonicAdventure2'' a few years later with something similar to the original snowboarding planned transition between Flying Battery and Ice Cap from this game happening in it.[[/note]]
** In a case of What Could ''Not'' Have Been, the Super Emeralds and their powers were not part of the original plan. According to [[WordOfGod Takashi Iizuka]] at [[http://www.youtube.com/watch?v=0nzxRoIX4QU&t=19m40s 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 ''VideoGame/SonicTheHedgehog1''. 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).