In the game's files are two unused texts regarding the Hylian Loach. This may suggest that said fish would've been found in both a bottle and without one.

The first text states:
"It's a Hylian Loach in a bottle!
An illusory fish that
few have caught...

And it came in a bottle!
What a find!"

Another one states:

"You got the Hylian Loach!
An illusory fish that
few have caught..."

In the game's files is unused text regarding the player's stolen Hero Shield. It's suggested that the shield would've been stolen, resulting in the player going to the Curiosity Shop to get it back.

"You bought back the Hero's Shield
that was stolen from you.

In the future, watch out for
swooping birds on your travels."

In the game's files are unused graphics that say "Game Over" and "Continue Playing?" In the final game, losing all of the player's hearts will warp said player back to the beginning area, and Spoiler:letting the moon fall will result in a lengthy cut scene followed by the famous words, "You've met a terrible fate, haven't you?" accompanied by the Happy Mask Saleman's chuckle.

In an article for the September 2000 issue of Nintendo Power, Jason Leung, the writer for the game's English-language script, claimed that the South Clock Town Business Scrub's allusion to his work keeping him away from his wife is a nod to the tribulations that the developers at Nintendo of Japan were going through while working on the game.

Depending on what you name your save file, the name inputted will act as a seed that determines the position of the twinkling white stars in the night sky, while the blue stars and larger red planet remain in the same position. Since there is a character limit of 8 characters for a name, the number of possible variations is estimated to be somewhere under 5.3 billion, the key word being "under" as this cosmetic feature does not utilize all 127 characters available, so the actual number is bound to be lower. This feature was explained to the Japanese audience at launch, but this was not known in the West until 2021.

If the Song of Healing in The Legend of Zelda: Majora's Mask is reversed, it sounds similar to Saria's Song from The Legend of Zelda: Ocarina of Time. While this may seem unintentional, the inputs to perform each song are also reversed from each other, with Saria's Song being played by pressing Down, Right and Left, while the Song of Healing is played by pressing Left, Right and Down.