According to Tropical Freeze's creative director Vince Joly, the development team had seriously considered including Enguarde the swordfish from prior Donkey Kong Country titles as a ridable animal buddy, but ultimately dropped him to focus more on the playable Kong characters.

One of the few tracks included from Donkey Kong Country: Tropical Freeze within the soundtrack for both Super Smash Bros. for Wii U and Super Smash Bros. Ultimate is "Swinger Flinger". However, actually listening to the track reveals it to instead be the theme for the Bopopolis stage.

This error is not presented in the Japanese versions of these games, where the "Swinger Flinger" track is properly referred to by its Japanese name equivalent to Bopopolis, ふみふみラビリンス (Fumifumi Rabirinsu), or Stomping Labyrinth. In comparison, the actual Swinger Flinger track and stage in the Japanese version of Tropical Freeze is called バインラビリンス (Bain Rabirinsu), or Vine Labyrinth.

If the Player backtracks at a certain point in level 4-3, The Amiss Abyss level, and waits a while they can see a one of the eponymous creatures of the Metroid Franchise floating in the background in silhouette.

This is true in both the Wii U and Nintendo Switch versions of the game

A string of text labelled "miiverse", found in the game files, suggests there was originally going to be an auto-post achievement system for when the player did certain things, similar to Hyrule Warriors.

At the end of the level, Aquedect Assault, the arcade sprite of the Original Donkey Kong can be seen in the background, much like Wonky Waterway from Donkey Kong Country Returns, only holding a Wii U Gamepad instead of a Wii Remote. Oddly enough this would be still the case with the level's appearance in the Nintendo Switch port of the game.

The Giant Squeekly from Crowded Cavern in Donkey Kong Country Returns can be seen frozen solid in the Background of the level, Blurry Furry.

At the second checkpoint in Fruity Factory, the background features a replica of Stage 1 from the original Arcade/NES classic, Donkey Kong 3.

Samus' ship from the Metroid series can be seen in the background of the Busted Bayou level.

At the beginning of level 1-1, Mangrove Cove, if the player turns around and enters the crashed plane, there will be a pile of four TVs. If Donkey Kong uses his ground pound move while near the four TVs, they will turn on. Two of the TVs will have the title screen for the English version of Donkey Kong Country: Returns playing, while the other two will have the Japanese version playing.

One of the items in Funky Kong's shop is a blue shield called the Crash Guard. His commentary on the item is a reference to the original Legend of Zelda: "Vehicle troubles? It's dangerous to go alone--take one of these!"

There's an old-fashioned record player in a hidden area at the end of World 1-3, near the secret exit. It strongly resembles Cranky Kong's record player seen in the original Donkey Kong Country, and will even play the same tune if the player pounds the ground next to it.

If DK is left idle for long enough, he will start playing a blue Nintendo 3DS XL, similar to to how he would play a grey Nintendo DS in DKC Returns. The audio heard from the system is actually from four real 3DS games by Nintendo:
• Animal Crossing: New Leaf
• Mario Kart 7
• Super Mario 3D Land
• Donkey Kong Country Returns 3D

In the Nintendo Switch port, this is only done when playing the Original Mode, as when playing that version's Funky Mode he'll instead be playing a Nintendo Switch system in handheld mode.