The playable characters of Shadow and Relm are father and daughter. Never stated directly in game, it is told through flashbacks when you sleep at an inn with Shadow in the party. Later, in 1998 a developer confirmed this in an interview, saying that the scene was to go as follows:

The final battle Spoiler:with Kefka references Dante Alighieri's Divine Comedy. Spoiler:The battle starts with a devil like creature (Hell), then goes on to a level with a number of people (Purgatory, where the souls wait to be judged). Then the party does battle with creatures that look like Michelangelo's Pietà (a sculpture of Jesus lying in Mary's lap after he was crucified). The battle concludes with a Kefka's angel in heaven. In the story, Dante asked God what the meaning of life was. This is mirrored by Kafka telling the heroes that "life is meaningless." It is also possible that Kefka is referencing Lucifer, who is known as a fallen angel. One of his attacks is called 'Fallen One,' which is one of the titles of Lucifer.

It's possible to play as General Leo in places you weren't meant to. Using the airship glitch (which is done by first getting the airship, flying around, getting back to the floating continent, saving, and then dying, giving you use of the airship to travel to any part of the world) you can skip getting a majority of the characters besides a select few. These character's slots will be replaced by characters only used in certain parts of the game, like General Leo.

There are multiple examples of art assets being censored in the North American release.
Esper Siren, Esper Starlet, Alluring Rider, Madam, The Goddess and Chadarnook's Godess part were all altered to be more acceptable to international audiences, mostly covering up more skin, or in Madam's case, removing smoking references.
Additionally, the Cafe sign originally read "Pub".
Many of these changes were kept in place in the Game Boy Advance port of the game.

There are three unused enemies hidden in the game's code. These are CzarDragon, Colossus and an alternate Umaro. The Colossus and Umaro use the same graphics and palettes as other enemies in the game. The Colossus is fairly simple and has a full attack script, and the alternate Umaro is weaker than the original.

CzarDragon however has no script, so when the battle begins, all it does is attack repeatedly. Which is odd, as there's a line of battle dialogue for the enemy, as though it was intended to be fought. The dialogue reads:
Mwa, ha ha... Humans and their desires! I'm free at last! I bring you destruction... I bring you terror... I am Czar... Prepare yourselves!
Taking into account the dialogue and its likeness to Shinryu in Final Fantasy V, it seems as though CzarDragon was intended to be an optional end boss. In the Gameboy Advance rerelease, CzarDragon can be fought under its original Japanese name Kaiser Dragon. It has a unique sprite similar to the SNES design.