In the 3DS version's files are unused models from the "Cook Kirby" Final Smash from Super Smash Bros. Brawl.

In the game's files are unused animations for when Giga Mac uses the attack for the KO Punch.

There's a rare glitch in the WarioWare Inc. stage. In normal gameplay, "Ashley's Song" plays its Japanese version in Japan only, and the English version in all other versions. However, in Spectate mode, if Player 1 is from Japan and this stage is chosen, the game will play the Japanese version of the song regardless of region.

This is the only game, as of this writing, where Marth does not say anything upon using the Counter move. The sounds for Marth's Counter voice clips can be heard in the game's Sound Test.

Inside the 3DS version's files are unused announcer clips for "Boss Battle," "Tourney," "Events," "Coin Battle," "Master/Crazy Orders," "Smash Tour," and "8-Player Smash," suggesting they may have been available for both versions. All of them except for Boss Battle would later be used for the Wii U version.

As for the 8-Player Smash, there is an announcer clip for "Yellow Team." However, because 8-Player Smash was cut for the 3DS version, so did the Yellow Team.

"Special Smash" can be heard in the Sound Test as voice clip 83 for the Announcer in the 3DS version.

There is an unused Announcer clip saying "Smash World," which may have been an early name for Smash Tour. Similarly, the Japanese name for Smash Tour is "World Smash."

Inside the 3DS version's game files is an unused sound for when you get a CD.

According to Masahiro Sakurai, in the November 2014 issue of GameInformer, the reason why both versions were released at different times was done to "keep the debugging schedules separate from each other:"

"The biggest reason was so we could keep the debug schedule separate from each other. Debugging a game this size is a major project involving hundreds of people, and since the two platforms offer pretty different content, we wanted to avoid conflicts during the debug stages. If we were hell-bent on a simultaneous day-and-date release, we would have wrapped up one title, put it on the back burner, and launched both games in 2015. But I doubt most people prefer that."

According to Masahiro Sakurai, in the November 2014 issue of GameInformer, the reason why Super Smash Bros. was released on two different consoles was because he was a “freelance game designer,” and that having a unique version of the game makes it fun.

"The first reason is that I think both portables and home consoles have their own traits that make them fun. I've gone into that in previous interviews, so I'll omit the details here.

One big reason for this approach is because I'm a freelance game designer ... I'm always going to be the center of any Smash Bros. project, but since I don't have my own personal studio, the staff changes in and out with each project. Changing development studios like this also means that you can't build out from the know-how and in-house assets you've accumulated over time.

As a development environment, it's different from a publisher that can work on fighting games, shooters, and open-world titles all at once. For us, even if things look the same, it's all completely different, completely built from scratch. If we started with a console project then moved on to the portable platform, once one team finished up their work, we'd have to wait and hand everything over to another team."

Smash Run mode was originally going to have cooperative gameplay, but the idea was dropped due to the 3DS's limitations.

On page 292 of the Prima Guide for Super Smash Bros. 3DS / Wii U, it shows a beta image of the roster containing the Mii Brawler icon. Although the individual Mii fighters do not have their own icons in the final game, the unused icons for the Brawler as well as the Mii Swordfighter and Mii Gunner can still be found in the game's data.

In the June 14th, 2015 Direct, Sakurai stated that the Suzaku Castle stage was the first in the series to have music that changes as the timer gets close to zero. This is false, as the Mushroom Kingdom stage of Super Smash Bros., and the Mushroom Kingdom and Mushroom Kingdom II stages of Super Smash Bros. Melee all have music that changes as the timer gets close to zero.

The reveal trailer for Roy shows him taunting in front of the Spicy Curry item. This is actually a reference to a Japan-only Super Smash Bros. Melee photo contest. The winner was a photo called "The Ultimate Curry", which depicted Roy taunting in front of the Curry food item.

The image of Mario and Luigi carrying gifts for Bayonetta is a possible reference to Bayonetta 2, in which Enzo carries Bayonetta's gift boxes in the game's opening cutscene.

If Little Mac accrues 100% of damage during a match, bruises and tape will appear on his face.

The match end tune from Street Fighter II can be found in the game's files. However, a remix of this tune was used instead for Ryu's win theme. The unused tune was most likely a placeholder during development.

Corrin from Fire Emblem Fates nearly didn't make it into the game because Super Smash Bros. creator Masahiro Sakurai thought that they had already included too many Fire Emblem characters.
However, Sakurai's team thought that Corrin would be a unique fighter and convinced him to include the character in the game.

According to Masahiro Sakurai, in an interview with Famitsu, the reason for the addition of the fighter Duck Hunt was for two reasons. The first reason was that he had an interest on adding them for a long time, but was also because of the uniqueness of the character. The second reason was because of the high sales of the game, and he deemed that the game was the high-selling shooting game in the USA.

The Epona trophy is taken from the 3DS release of Ocarina of Time, rather than the original Nintendo 64 release.

In the Taiwan and Hong Kong websites of the Super Smash Bros. for Nintendo 3DS websites, one of the photos is actually taken from the Wii U version. The Wii U version was not released in Taiwan or Hong Kong yet, and was likely just an oversight of the developers.

The promotional artwork for Ryu is a reference to the Street Fighter 2 World Warriors arcade artwork.