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.

In the Boxing Ring stage of the Wii U version of the game, character aliases appear on the screen in the background which reference other games or early concepts, such as Mario's being "Mr. Video Game Himself" referencing his early name "Mr. Video", and R.O.B.'s being Spoiler:"The Last of His Kind", referencing the events of Subspace Emissary from Super Smash Bros. Brawl in which Spoiler:the other R.O.B.s were destroyed.

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 Pokémon palette as apposed to her shiny palette. This is most noticeable in her eye color.

According to Masahiro Sakurai, the Orbital Gate Assault stage took one year to create.

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".

When initiating Palutena's Guidance as Pit when fighting against a Mii Gunner, the Nintendo Wii's code name "Revolution" is referenced when Viridi refers to the Mii Gunner's motion controlled arm cannon as "revolutionary".

When initiating Palutena's Guidance as Pit when fighting against Shulk, Pit will quote several popular phrases used in Xenoblade Chronicles, such as "What a bunch'a jokers" and "Let's not lose our 'eads, though."

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.

During Palutena's Temple, Palutena, Viridi and other characters from Kid Icarus: Uprising will converse with Pit about the character you're fighting against. This is similar to how Snake in Super Smash Bros. Brawl could use his codec to converse with either Colonel Campbell, Mei Ling, or Otacon when on Shadow Moses Island.

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.

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.

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.

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?"

The Pokemon Trainer trophy makes reference to the first opening theme music from the English dub of the Pokémon anime.

"Pop quiz! What do Misty, Brock, Cynthia, Iris, and Ash all have in common? That's right"”they're all Pokémon Trainers! This Pokémon Master in the making is the same. Back in Super Smash Bros. Brawl, he fought to be the very best"”like no one ever was. To smash them was his real test"”to launch them was his cause!"

The song that plays on the results screen after a fight is the character select theme from the first Super Smash Bros.

Sometimes when Luigi uses the green missile and he hits a wall, he will stick to the wall.

According to Masahiro Sakurai, the reason the Ice Climbers were cut from the roster is because of 3DS hardware limitations. He also states that he didn't want to add them exclusively to the Wii U roster to avoid there being considerable differences between the two versions.