After you go to Zozo and meet Ramuh, when it tells you to choose your party members and Celes and Locke are required, if you switch Locke out of the box it won't let you put him back in (not sure if the same happens with Celes), and when you go to Narshe to change your party, he no longer appears in the character choice screen, he has just disappeared from the game. The only way I've found to fix this is to reset and start from your last save point.
Be very careful when using Relm's sketch ability in the U.S. SNES version of the game. If it fails on some enemies, an uninitialized pointer will cause a bug and mess with the game data, possibly even corrupting save files. If you're using an emulator it's easy enough to avoid this using save states, or just save often. Since Relm is not required for any sequence in the game except briefly being in your party when exiting Esper mountain some players choose to not bother using her partially for this reason. However in some cases if you flee from the battle and save it immediately, you can reset the game and it should work fine, but you will find your inventory is glitched with massive amounts of rare/unique items that some people believe is worth the risk
Returning to the World of Balance
Early versions of the cartridges for this game featured a bug by which it was possible to return to the world of balance from the world of ruin. In the walkway above the Opera House, where Ultros pushed off the 4 ton weight there are a number of rats running around the scaffolding. If the party lost to them in the world of ruin they would be returned to the Opera House in the world of balance just as if they had failed to prevent Ultros from dropping the weight. After performing this glitch however, the only way to return to the World of Ruin was to ride Figaro Castle underground, and there would be no airship in the World of Ruin.
Due to errors in programming, the Evade stat is totally useless. Magic Evade affects both Evade and Magic Evade. As a result, the Blind status effect has no effect on reducing the accuracy of a physical attack, and Beads have absolutely no use at all. In addition, while certain statuses (Haste, Slow, Life 3, Poison, Seizure, Near Fatal are a few examples) are meant to affect hit rates, they're not in use.
This is probably the most well-known and most useful out of any of the bugs in the game. The trick comes in realizing that any creature with the "vanish" status has very poor magic defense and it is affected by virtually all spells, including Doom and X-Zone which offer instant kills. Many powerful enemies most of the bosses in the game can be instantly killed by casting vanish on them and then casting Doom or X-Zone including Intangir which is used to net in 10 magic points. Doom only affects one enemy, whereas X-Zone affects all enemies. The Vanish and Doom spells can be learned in the world of balance after finishing the magitek factory. The X-Zone spell can be learned in the world of ruin after fighting Phunbaba for the first time.
The best known use for the trick is just using X-Zone to instantly defeat Wrexsoul in Cyan's sidequest, since it will kill both SoulSavers (no Vanish necessary), and end the battle (The SoulSavers regenerate themselves immediately after they're slain). In general most bosses can be easily defeated by casting vanish on them then Doom or X-Zone, although this might decrease your enjoyment of playing the game. Also, if you use Vanish and X-zone on Doom Gaze, it won't drop you the Bahamut Esper (However, if you use Doom after Vanish, you will still obtain Bahamut).
Technical Details of how Vanish/Doom works: Certain enemies (such as most bosses) has a special bit that determines whether they can be hit by Instant-Death spells or not. Most Instant-death spells (as well as Dischord and gravity based spells such as Demi, Shimsham, Sonic Boom, Grav Bomb) automatically misses if this bit is set. However, when the game determines whether a spell hits or not, it checks for Vanish first. Therefore, when you Vanish an enemy then cast a spell, it will always hit no matter what. NOTE: Most enemies also have protection from certain statuses, meaning you can't inflict the status on the enemy (For example, Vargas is protected from Poison status, meaning you can't set Poison on him, ever). Therefore, if you use, say, Mute, after vanishing the enemy, the spell WILL hit, but will do nothing because the enemy can't be muted. This is evident if you use Vanish+Imp on an Imp-protected enemy, as the spell will hit and change the enemy's graphic to that of an imp, but the enemy will act as if it's not Imped because Imp isn't actually set on the enemy.
Confuse+Smoke Bomb Glitch
This is a glitch that is used in the 2006 gameboy advance version of Final Fantasy VI. This trick works by first casting confuse on the character who is about to use the "Smoke Bomb" item. As the character gets hit by the confuse spell quickly use the "Smoke Bomb" item and the character will be confused which causes your confused character to use the smoke bomb item on the enemy party and the enemy will be caused to instantly escape from battle. This trick works on the Intangir enemy which is used to net 10 magic points since you cannot cast Vanish and Death in the Gameboy advance version of the game. Once in a while the spell will miss and the character will just use the smoke bomb item on the ally party.
A name to a glitch that allows Cyan to attack enemies over and over again. First, Cyan must use Retort. Next, he must be turned into an Imp, and killed with a physical blow (he can be weakened with Magic attacks, but the killing blow must be physical. If Cyan is attacked physically before he is killed, he must use Retort again). Now revive the dead, Imped Cyan, and have anyone use the Fight command. Cyan will begin to attack over and over again.
This glitch combines two other glitches. One if that is Cyan is killed by a physical blow while having the "Retort" status, when revived he will use Retort in response to any attack, even one that does not hit him. He'll use Retort even if he himself attacks.
The second glitch is that an Imped Cyan cannot use Retort, so he will use a normal attack instead. By combining these glitches, "Psycho" Cyan goes into an infinite loop, attacking and responding to his own attack with another attack, over and over, until all the enemies are dead.
This glitch can be performed in the Game Boy Advance version, albeit a little differently. First, kill Cyan. Then revive him. Next, have him perform Sky (aka Retort). Finally, Imp him.
Permanently Morph Terra
First, have Terra Morph. Then have another character use Quick. While the character casts their second command, let Terra's Morph meter run out. After the Quick effect runs out, Terra will remain in Morph despite the fact her Morph meter is depleted. This occurs because other characters cannot perform actions while Quick is in effect. Thus, Terra will not be allowed to Revert back when her Morph meter depletes. She will remain in Morph for the entire battle, unless killed.
Shadow (or Relm) may randomly have Interceptor block an attack on them. By using "Rippler", this status can be swapped to another character. But if Interceptor is Rippled to an enemy, and that enemy is killed, Interceptor will be lost forever.
2 Shadows on The Floating Continent
Go to the Floating Continent, and, without getting Shadow, go through the entire continent all the way to Atma/Ultima Weapon, and beat him. Now, *WITHOUT SAVING AND WITHOUT GETTING BACK ON THE AIRSHIP*, turn around go all the way back to the beginning where Shadow is waiting for you. You can't save at the last save point because once you go down the air funnel everything resets and you can't walk back because the giant wall is raised up. Once you get back to square 1, grab Shadow, then save at that point. Go through again (After you've completed all the puzzles it really only takes about 3 or 4 minutes to go each way). Staying away from the airship, take Shadow (as your main leader, for graphic's sake) and the party up to the statues. There will be 2 Shadows on the screen when the actual Shadow jumps down to help Celes. With 4 characters in your party some weird things happen. Only 2 - 3 characters are supposed to be stunned by the statues, and so the person in slot 3 seems to vanish. Once Kefka does his damage you have Shadow in your party to help escape the contintent.