During the song "Master Core" (which plays when fighting the identically-named boss in Classic Mode), the instruments will silence after 1 minute and 53 seconds and a series of beeps will play for six seconds before the instruments start playing again. These beeps are Morse Code for "MASTER CORE".

If Shulk is on the Gaur Plains stage when Metal Face appears, Metal Face will occasionally say unique taunts.

The taunts are:
• "If it isn't the puny boy himself.You miss me?"
• "Hey, Monado boy, I don't think you can hurt me with that thing"
• "OH! It looks like Monado boy's been practicing"
• "If the brat's here, I bet Dunban can't be far behind."

The amiibo figures sold alongside the game are well known for having a number of defect units. These include, but are likely not limited to:
• Samus having 2 cannons instead of 1.
• Marth having 2 swords instead of 1.
• Peach having no legs.
• Luigi missing his left hand.

When Pit gets KO'd he'll sometimes say, "I'm Finished". This is a reference to the original Kid Icarus Game Over screen.

The trophy for the Lurchthorn enemy from Kid Icarus: Uprising references Superman. The first sentence reads, "Is it a bird? Is it a plane? No, it's... some kind of giant fossilized fish."

While Xander Mobus, the game's announcer, recorded a shout of the game's name (much like Super Smash Bros. Melee), it went entirely unused in the final game's release.

Unlike all previous entries in the Smash Bros. series, Jigglypuff uses the standard Pokemon palette as apposed to her shiny palette. This is most noticeable in her eye color.

The description for the "Souflee" trophy from Kid Icarus reads, "We could tell you it's a cake, but that would be a lie". This is a reference to running gag through the first Portal game, stating that "the cake is a lie".

Lucina is the only unlockable character who was officially revealed prior to the game's 3DS release and is the first female unlockable character in the Super Smash Bros. series.

Originally, Flying Man had both a 2D and 3D model for when he appears on the Magicant stage. The 3D model was scrapped however, to lessen strain on the 3DS hardware.

Jigglypuff's character model in the 3DS version is recycled from the model used for Jigglypuff in Pokemon X & Y.

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.

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 UK 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.