* 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.
* FanRemake: ''Sonic 3 Complete'' is a fairly well-known hack that polishes the game in areas that the official ''Sonic 3 & Knuckles'' didn't (fixing glitches, giving Super Sonic actual sprites for certain things) as well as allowing several option like choosing the different 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''.
* ManualMisprint: A few of the enemies from ''Sonic & Knuckles'' showed up in ''Sonic the Hedgehog 3'''s instruction manual.
* 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, 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).
** There tends to be confusion as to why the original ''VideoGame/SonicTheHedgehog'' could not be locked in with ''Sonic & Knuckles''. The two most popular explanations are Knuckles would have dramatically altered the color pallet 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 in Sonic the Hedgehog 1'' as well as any future ROM hacks starring characters other than Sonic.
** Despite what your third grade friends (and basic logic) told you, it's not possible to beat the 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.
* WhatCouldHaveBeen: Flying Battery Zone was originally planned to be in the ''Sonic 3'' half, between Carnival Night and Ice Cap (and Sonic's snowboard would have been a door from the Battery). But time constraints intervened, and it had to be cut and moved to the ''Sonic & Knuckles'' half. Additionally, Mushroom Hill (then known as Mushroom Valley) was also planned for the ''Sonic 3'' half.