There are several unused enemies and enemy behaviors. The unused enemies include a Red Bullet Bill and Cannon, a double swap platform and a Bloo Blah holding a Piro Dangle. The unused enemy behaviors are Egg Plants spitting bubbles at a regular interval and three Cactus Jacks falling down and forming a stack.

When approaching the boss Naval Piranha, the player can see him in his un-transformed state and can fire an egg at him. Doing so results in him dying instantly, and Kamek flying in to yell "OH, MY!!!" before flying away in retreat.

An unused monkey enemy can be found in the game's graphics. They look to be similar to Donkey Kong in the style of Yoshi's Island, including a barrel that would have presumably been thrown.

There are a number of unused transformations in the ROM that never made it into the final game. These include a plane, a mushroom and a tree.

In May 1995, an interview with series creator Shigeru Miyamoto and Rare co-founder Tim Stamper about the development of Donkey Kong Country (DKC) was published in the magazine Electronic Games, conducted by game journalist Steven L. Kent. Kent later claimed on an episode of G4's docuseries "Icons" that Miyamoto was angry during this interview, channelling it into bitter criticisms of DKC's gameplay and the Western market's praise of its pre-rendered graphics, and that Stamper "sat there and took it, even though really the anger wasn't meant to be at Stamper". Miyamoto clarified in a 2010 interview with IGN that he did like the game despite these rumored criticisms, and that he worked closely with Rare and Stamper during development.

Years after the interview's publication, Kent would print an alleged portion of a later interview with Miyamoto in his 2001 book "The Ultimate History of Video Games", claiming that the anger had stemmed from "touchy" internal discussions regarding Super Mario World 2: Yoshi's Island. The hand-drawn crayon art style of that game was said to be a result of the alleged anger over DKC's graphics causing him to rebel against Nintendo's internal evaluation committee, who wanted Yoshi's Island to use pre-rendered graphics. Part of the Miyamoto quote reads:


Yoshi's Island director Takashi Tezuka would deliver a less angered statement that may be related to these claims in a September 1995 interview with the magazine Dengeki Super Famicom. He claimed that the choice in art style was done for sentimental reasons, as the developers believed that all video games from that point on would likely utilize 3D graphics, and wanted Yoshi's Island to be a bow-out for 2D graphics:

There's a part of the background in world 4-1 that appears to take the shape of a topless woman's torso.

In the German version of Yoshi's Island, Naval Piranha is named "Audrey", referencing the 1960 film "The Little Shop of Horrors".