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.

Donkey Kong's sprite on 75M in Super Smash Bros. Brawl and Super Smash Bros. for Wii U has a tan skin tone, which is different from DK's paler sprite in either the NES or arcade versions of Donkey Kong. This appears to be the result of Nintendo using an image of the game's arcade version originating from a Japanese retro gaming fan site called Muu-World as reference material, as that image seems to have a color error that makes DK appear tan. The English-language fan wiki Super Mario Wiki has been hosting a different Donkey Kong screenshot with the same error on its page for the game since 2005, and the source of the error as well as several of the images featuring it (including the Mario Wiki screenshot) is currently unknown. It also gives DK a coincidental resemblance to the appearance on the box art for NES Donkey Kong and in-game in Atarisoft's Commodore 64 Donkey Kong. This was fixed for Super Smash Bros. Ultimate.

On August 18th and 19th, 2014, several weeks before Super Smash Bros. for Nintendo 3DS launched in Japan, one of the most influential leaks in the series occurred. Footage of the gameplay and the roster (including fighters who were not announced by Nintendo at the time) were uploaded to 4chan, and then YouTube. The legitimacy of the leaks were brought into question by fans (such as the consistency of the rosters compared to the one that was shown at E3 that year), with some speculating that the leaks originated from an employee connected to the Entertainment Software Ratings Board (ESRB), leading fans to refer to the leak as the ESRB leak. It was not until Nintendo took down the YouTube videos very shortly after they were uploaded when they were confirmed to be legitimate. Days later, Shulk would be revealed for the game in a Japanese Nintendo Direct, confirming the rest of the game's unannounced roster.

In 2023, it was discovered that the leaker was a child of a Nintendo of America employee. According to a DidYouKnowGaming? video researching the history of various video game leaks, the employee recorded footage of the game in action, which would be sent to the ESRB for review. The child gained access to it and shared the footage with his friends, before spreading out of control. Nintendo of America fired the employee shortly after word got out.

Within the game's data is an unused placeholder Masterpiece banner for the original Super Smash Bros. The banner is located in the game's files alongside those for the other Masterpieces, which together with its filename, "soft_50_SuperSmashBros.nut", indicates that it is meant to represent the game rather than being a failsafe. Furthermore, the placeholder nature of the graphic and the lack of any other assets related to it indicate that the demo was removed relatively early into development. As no Nintendo 64 games are featured as Masterpieces in Super Smash Bros. for Wii U, this would have made Super Smash Bros. the only game to hold this distinction.

Roll's trophy contains modeled and textured undergarments beneath her dress; however, this is obscured in typical gameplay by a black void. This notably differs from Peach's trophy, which features similar censorship but has the black void baked into the model (with no additional graphics hidden underneath).