Gotta say, this is the biggest "I forgot how things used to be" topic around here.
Chances are you aren't playing Ultimate Mortal Kombat 3 then, because Chameleon will try to show up quite often in the genesis edition, but of course the game will eventually crash because he wasn't finished for that game. You wouldn't want to be a powerleveler in Phantasy Star IV either, that could break the game. But for those 2 are the bugs I know about for that era.
What I do know is that several other games have had glitches ranging from unimportant to game breaking, and they would never be fixed because patching wasn't a thing for consoles/arcades. The first edition of Super Mario Sunshine is uncompletable. Metroid Prime 2 has a gamebreaking bug, and unlike UMK3 it takes more than just a few fights to get back where you were when that bug may take place. Paper Mario (N64) crashes rarely. Prince of Persia Two Thrones (GC) crashes hard if you make a time paradox. A few mainline Pokémon games on GBA have a time limit glitch.
Some games also performed worse than developers and publisher intended, "forcing" both publishers and consumers to spend more money to "fix" those problems, as what happened to games such as Metal Slug 2, Virtua Fighter 2 and Castlevania 64; those 3 at least could be fixed if patching was a thing for the platforms they were in.
And then there are situations in which one edition of the game is simply inferior to the other, such as what happens among regional versions of Luigi's Mansion (GC).
So, just imagine the situation: you buy a GameCube at launch date and get yourself Super Mario Sunshine and Luigi's Mansion. Your chances of having gotten both a faulty copy of Sunshine and the inferior edition of Luigi's Mansion are high, and no patch would have helped that because the technology wasn't there yet.
