In an interview with Nintendo Dream, Masahiro Sakurai stated that the reason why Ness and Lucas's final smashes, PK Starstorm, function differently from their Brawl counterparts was due to limitations in the 3DS hardware.

Yoshi unlike other games in the series does not make any noise upon using his "Yoshi Bomb" down special. However, the voice clip can be found as Clip 22 in his section at the Sound Test.

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.

Mewtwo's character art uses the same pose as the one in Super Smash Bros. Melee.

Leaked screenshots show that there was originally a trophy for Tharja from Fire Emblem Awakening, but it was removed from the final game. Some speculate this was because of her suggestive clothing that would have likely given the game a more mature rating from the ESRB. There has been no confirmation that this trophy was ever set to appear.

Takamaru was once considered as a possible playable character in Super Smash Bros. for 3DS and Wii U. According to Masahiro Sakurai, due to his low popularity, he was included as an Assist Trophy instead.

There is a glitch in the 3DS release that allows Yoshi to grow infinitely larger. If a Yoshi eats and re-lays a big Yoshi, the larger Yoshi will hatch larger than before.

After obtaining every Mii outfit, the game will give you a notification reading, "Collected every type of custom outfit! Your body is ready!" A reference to Nintendo of America CEO Reggie Fils-Aime's popular quote from E3 2007, "My body is ready!", which has since become a popular meme.

When pausing the 3DS version during a match, the player models are switched to a higher resolution version of the fighter's model. Within the game's data are 2 models for each figher, both paused and unpaused.

In the Magicant stage, a stage hazard called the Flying Man can be recruited by players to fight alongside with them until it gets knocked off stage by another player. Each time the Flying Man is defeated, a tombstone appears near where they would normally spawn. Once five tombstones have taken place, the Flying Man will no longer spawn during the round, much alike their roles in EarthBound Beginnings/Mother and Earthbound/Mother 2, in which five of them are recruitable and will not come back once they are defeated, signified by the addition of tombstones near their house as each one dies.

According to the game's director, Masahiro Sakurai, the reason for Sheik and Zero Suit Samus appearing as separate characters is due to the limitations of the 3DS not being able to have them transform from their respective characters. This option was made because Sakurai wanted both versions of the game to have same roster.

In the North American version, the Mario Kart Shy Guy trophy states that he made his racing debut in Mario Kart 7. This technically is false, as Shy Guy could be played in Mario Kart DS, but only in Download Play for players who didn't own the game. This was fixed in the PAL version by stating he was first selectable in Mario Kart 7.

The StreetSmash minigame is very similar to the Smash Ride minigame from Kirby: Squeak Squad, another game developed by HAL Laboratory.

There are actually two different versions of the Balloon Fight stage. The layout is selected randomly, but the alternate form can be chosen by holding down the L button when selecting the stage.

Holding down the L button when selecting the Boxing Ring stage will change the design of the ring from Punch Out oriented to Super Smash Bros. oriented.

Having specific character pairs fight each other in a normal 1v1 Smash fight results in personalized victory screens:

• Fox beats Falco:"Better luck next time, Falco."
• Falco beats Fox: "You're off your game, Fox."
• Male Robin beats Lucina: "Lucina, I hope I didn't hurt you."
• Female Robin beats Lucina: "How can you protect Chrom if you can't protect yourself?"
• Lucina beats Marth: "This is the Hero-King?"
• Lucina beats Ike: "And they call you the Radiant Hero?"
• Palutena beats Pit:"Oh, so sorry about that, Pit."
• Palutena beats Dark Pit: "Poor little Pittoo."
• Dark Pit beats Pit: "Where's your goddess now?"

As the Villager does their final smash attack, Tom Nook actually throws furniture into the house being built. There's even a chance he will throw in a Triforce from The Legend of Zelda, as it can be collected in some of the Animal Crossing games as a house decoration.