There are a number of unused audio clips still present within The Minish Cap. Many of these unused pieces are renditions of songs and sound effects from previous games (e.g. the Lost Woods from Ocarina of Time, attached).

In the first dungeon, you come across a red-capped mushroom enemy that walks around spraying spores. The enemy is named "Puffstool", and is actually a reference to a boss found in Pikmin also named "Puffstool" who sprays spores to infect Pikmin and turn them against you.

In the code of the ROM is what appears to be a man wearing a pair of underpants, a cape, and a crown. It's very out of style and obviously just a scribble, but it also includes a full walking sprite-set, as well a number of other random animations.

The Ocarina of Wind's tune is the same as the Warp Whistle from Super Mario Bros. 3 and the Recorder from the original The Legend of Zelda.

Bob-ombs from the Mario series make a cameo as dungeon enemies.

In the opening cutscene of the game, the story tells that a "tiny Picori appeared from the sky, bringing the hero of men a sword and a golden light". According the the official Legend of Zelda timeline, The Minish Cap is the second game chronologically, taking place only after the events of The Legend of Zelda: Skyward Sword. This might suggest that the Picori is the incarnation of Link from Skyward Sword, bringing the master sword down from Skyloft. In addition, the man brandishing the sword in the mural that is depicted as the text displays appears to be some incarnation of Link.

Malon, who sells Lon Lon milk in Hyrule Town, can be heard singing Epona's Song from Ocarina of Time when you are near her.

There's an unused animation for the decorative mailbox that appears above the post office in Hyrule Castle Town. The level of animation suggests that there were to be fully functional mailboxes in the game, much like with The Wind Waker.

In the PAL version, the description for figurine #108, Ice Wizzrobe, suggests hitting Ice Wizzrobes with the Fire Rod, an item not available in the final version of the game. This was corrected in the USA release.

In a cave digging in Castor Wilds, the Japanese word "もぐら" ("Mole") is hidden out of the game's visible area.

Vaati's laugh is just a shortened version of the Happy Mask Salesman's laugh from Majora's Mask.

The European release's music in the Sword Dojo is a bit different from the Japanese and US releases. The reason for this change is unknown.

Hyrule Castle has three unused stain glass windows of three characters from the The Legend of Zelda: The Wind Waker:
•The Deku Tree
•Valoo
•Jabun

In Hyrule Town, three travelers in the lobby of the Happy Hearth Inn, named Din, Nayru, and Farore, are the same characters as the Oracles from The Legend of Zelda: Oracle of Ages and The Legend of Zelda: Oracle of Seasons. They are each looking for new homes to move into, which is the basis of an optional side quest that can be started after completing the Fortress of Winds. Gorman will now be renting out a house to tenants, and Link can convince one of the travelers to move in and obtain a Charm from that traveler. Afterwards, if Link fuses Kinstones with Bremor, Mutoh will become motivated to build a second house for Gorman to rent out. Link can then convince one of the remaining two travelers to move in, and will obtain their respective Charm. Each of the two houses built have a red roof and a blue roof, reflecting the color schemes of Din and Nayru respectively. However no third house can be built in the game, leaving the third Oracle homeless and stuck in the inn's lobby. In the European version of the game, Gorman makes a comment about wanting to build a house just south of the Royal Hyrule Library, on a plot of land occupied by cats, but he never does. This comment was removed from the North American release of the game which came out two months later.

Although the choice of who will remain homeless is entirely up to the player, the most probable canonical traveler to remain homeless is Farore. This is based on the lack of a green-roofed house to reflect her color scheme, her figurine description noting that she is bothered by people who "take advantage of her kind nature" (unlike Din and Nayru's descriptions which only point out where they are from and are looking for a new home), and by the development history of Oracle of Ages and Seasons, which was originally planned to be three games with each focusing on a different piece of the Triforce represented by a different Oracle, although only two games centering on Din and Nayru would ultimately be developed.

It's unknown if this incomplete side quest was an oversight, or if it was an intentional in-joke by Capcom, who developed both The Minish Cap and Oracle of Ages and Seasons.

In an interview featured in the 124th issue of the Nintendo Dream magazine, the game's director Hidemaro Fujibayashi explained that the character Ezlo was created because in The Legend of Zelda: Oracle of Ages and Seasons, there wasn't any character that could explain things to the player and the development team felt players were disadvantaged because of this. He stated:

"At the time that we were making the Oracle games, we really struggled with the lack of a character like Navi in 'Ocarina of Time' that could explain the situation. So from the beginning, we had decided there would be a companion character on the next adventure".