Due to the music being pre-recorded, the developers created NES-style chiptune versions of every song in the game in order to fit within the memory limitations of Download Play (which allows up to 3 players to play together with a single copy of the game). They believed that players would want to hear this music at times other than using Download Play, so they created the Timeless Tunic, an outfit that enables the chiptune music and turns Link into a blocky, "retro"-styled character.

There is an unfinished and unused outfit remaining in the game's data, that gives Link a pair of Great Fairy wings, prosthetic antennae, and a Kokiri-like tunic. It appears to be from an early stage in development since it has Link's hair and body proportions from A Link Between Worlds, with the "Toon Link" facial features used in Tri Force Heroes.

Link is incorrectly shown as right-handed at two points in the game: The "Item!" communication icon, and a piece of artwork during the game's ending.

Madame Couture is actually singing her own shop's background music. Her vocals are removed from the music whenever she speaks to the player.

The Legendary Dress was called the Zelda Dress in earlier builds of the game.

Promotional artwork for the three Links in a Totem was altered before release, with Red Link's expression being changed from stressed to startled.

There were numerous outfits, including the Emperor's New Clothes outfit, which did not make past the planning phase. These include a "Stinky Costume which would keep enemies at bay", a "Kansai Outfit which would put the situation reports into the Kansai dialect of Japanese", and a "Handsome Outfit that made you look really cool in photos".

In the lobby of Tri Force Heroes the player can dash into a wall on either side of the room and a purple and pink striped ball will drop down. If the player hits the ball into the air it will start playing music from various games in the series. The music will only continue if the player keeps the ball in the air.

The developers wanted to include a costume for Link that was based off of the tale "The Emperor's New Clothes", where the Emperor believes he's wearing the most wonderful clothes ever, but is in fact naked. However, they weren't able to think of any abilities for the outfit, so the idea was left out.

During development, game director Hiromasa Shikata said that a four-player totem would be "too tall", which is why only three Links are usable.

In the North American localization, when reading one of the ancient bookshelves, it reads
"Still, coming here has at least afforded me the rare chance to explore these ancient ruins. So ancient. Such ruin." This is a reference to the popular "Doge meme". The European and Japanese localizations of the game, however, have no reference to the meme.

According to the game's developers, the time placement of the game within The Legend of Zelda series is several years after the events of The Legend of Zelda: A Link Between Worlds. The Link in Tri Force Heroes is also the same one from A Link Between Worlds.

An idea for voice chat which was considered was to have players chat between the experience gap of other players, where experienced players could instruct inexperienced players what to do. However, Hiromasa Shikata and Eiji Aonuma found their enjoyment levels with this feature to drop.