In the level Poisonous Pipeline in KAOS Kore, Dixie Kong, Kiddy Kong, Enguarde, and aquatic enemies are depicted swimming in the poisonous water. In reality, it would be lethal.
The helicopter only has 1 rotor. A helicopter needs at least 2 rotors to fly.
The boss level Belcha's Barn at Lake Orangatanga, despite taking place inside of a mill, the original SNES version has the factory background like the later levels Fireball Frenzy, Blazing Bazukas, and Krack-Shot Kroc that are all factory levels. This was corrected in the GBA remake in order to be consistent with mill-type levels and their matching backgrounds.
When switching positions from Kiddy Kong to Dixie Kong to be in the lead, the sound effect typical of switching the Kongs' positions is immediately cut off with that of Dixie Kong popping her bubble gum before it can be fully heard when on land (SNES version).
The level Demolition Drain-Pipe uses the Toboggan that's also used in the later level Tearaway Toboggan as a means of venturing through the level, which can cling onto railings without any use of hooks or whatever means that would be impossible to do without.
The level Rocket Rush in Krematoa is missing the letter G in K-O-N-G in the North American version of the game. This is fixed in the Game Boy Advance remake for all regions.
The artwork of the second boss battle Arich's Ambush is shown taking place inside of a hollowed-tree. In the actual game, the battle takes place on tree limbs between two trees.
In one of the game's group artworks, Cranky Kong is shown playing the Nintendo 64. He does not play the Nintendo 64 in the game and only appears as a CPU-controlled rival to Dixie Kong or Kiddy Kong in Swanky's Sideshow and in the game's special ending after freeing the Banana Bird Queen, only Wrinkly Kong plays the Nintendo 64 whenever visiting her namesake Save Cave and one of her quotes states that she's glad her husband Cranky doesn't know about it and fears he too will be addicted to it.
In the group artwork of the Kong Family checking out the Nintendo 64, Wrinkly Kong is depicted wearing a green shawl like she does in Donkey Kong Country 2: Diddy's Kong Quest. However, she wears her purple workout outfit in her solo artwork and in the game when the player visits her Save Cave.