A hidden programmer message is hidden in the files of Disk 3, stating:

"great special thanx to you, ARIKO...from your husband, HIDEJI".

On January 17, 2022, the Italian Senate hosted a Zoom meeting about the Transparent Public Service. Just when Nobel Prize-winning physicist Giorgio Parisi was about to be introduced, a user named Alex Spence "zoombombed" the meeting with at least 30 seconds of a CG pornographic video featuring Tifa Lockhart that was originally made by Patreon user JuicyNeko. The news spread mere days after the incident, and Tifa became the subject of memes that associated her with Italy, including being considered an Italian video game mascot that’s on par with Mario.

In the Japanese version, the test battle in the debug room features a proper background and models for the enemies included (borrowed from other enemies), whereas the international version simply pits the party against yellow pyramids in a black void.

Additionally, the very first Japanese release contains an unfinished eleventh section of the debug room, left over from an earlier build of the game. Because the game's code changed significantly since that build, much of the eleventh section is broken: Cloud's model does not show up (though he is still able to move around and interact with the NPCs there), text is corrupted, and the background music is a heavily distorted version of Aeris' theme.

If you encounter the enemy Adamantaimai and manage to cast Barrier, MBarrier or Big Guard (which includes both statuses) before its first turn, the Adamantaimai will attempt to use Cure. However, it does not have Cure in its attack list, which will most commonly result in a debug error message appearing advising players to hold L1, R1 and Select to return to the overworld. The reason Adamantaimai tries to use Cure is because Cure has the ability ID of 0. Adamantaimai selects an ability to use if it lacks Barrier status, and it can select another ability if it has Barrier but not MBarrier (at no other time does this enemy store an ability in memory). However, no value was ever set for the possibility of it already having both statuses on its first turn, so it never sets an ability and instead tries to use the ability set at 0. While Adamantaimai using Cure is not unusual on paper, it has no animation for it unlike its other attacks, resulting in the error message. Attempting this glitch in modern releases of the game will cause it to freeze.