In the final battle against Zeromus, Edge can steal an item known as Dark Matter in the Japanese version of Final Fantasy 4. This item, long thought to reduce the damage of Zeromus's Big Bang attack, is actually a joke item. In the DS version, a superboss named Proto-Babil appears if you use this item on the face of the Moon.

In the version 1.0 release of the game (which only exists in Japanese), there was a bug that occurred when exiting certain areas of the game that messed with the game's RAM address of which location the player was in. Due to this, when exiting certain dungeons and then flying to the underworld, the game would think you were inside a lunar dungeon and read from the wrong set of enemy AI tables when entering battles. Due to this, enemies will spend the entirety of the battle using Stone on themselves and their teammates until all of them are defeated. The only difference between versions 1.0 and 1.1 is a bugfix for this.

In all versions of the game there is a secret passage in Cafe HOWDY!/Pub Lali-Ho in the Dwarven Castle of the Underworld that leads to a place called the "Developer's Room". In it are recolored sprites that are meant to be the developers of the game. In the DS release, it has the developers of the DS remake instead. This area was cut in "Final Fantasy 4 Easy-Type" and "Final Fantasy 2 (US)" because it's possible to find a pornographic magazine in the room, called Lustful Lali-Ho.