The texture of the Metroid assist trophy contains a sprite of EarthBound's Mr. Saturn. It can't be seen in-game, as it isn't mapped to the model.

Marth's trophy information is not entirely correct, as it says Altea was destroyed by Akaneia. In actuality, Akaneia only controlled Altea for a period of time, and is reclaimed by Marth near the end of the game.

The stage "Green Hill Zone" has a large amount of extra geometry outside of the camera view, a fact that the game's director, Masahiro Sakurai, noted on the Smash Bros. Dojo when the stage was revealed.

An unused character select screen menu exists in the game for a wi-fi version of Boss Battles. It is unknown if this mode is functional and why it goes unused.

The description text for the mode reads:
"Take on 10 bosses with the help of a friend! (2 players)"

Kirby has an unused animation that appears to be him walking with a hammer and then swinging it with full force in the same manner as King Dedede's Jet Hammer move. Kirby charging up and releasing his hammer is something he would later be able to do in the next game of the series onward.

Fox and Falco both have unused animations that appear to be their blasters misfiring.

The "Shellcreepers" trophy states that Mario and Luigi used to fight these enemies "back when they were plumbers", though there has been no actual mention of them retiring throughout the Mario series.

Solid Snake can be seen hiding inside the Cardboard Box trophy.

There are unused CD labels in the games files, stored with the data for the CDs that are found during battles. It is likely that the CDs were originally intended to show these labels related to what would have been unlocked when collecting them.

The Primid's faces in the Subspace Emissary change every time the game is started.

There is some red text written in an empty area of Snake's head texture near the hair tufts. The text reads "def n_f_o layer" and is hidden by alpha transparency. The text can also be found for each of his alternate colors.

Wolf has an unused attack animation which looks similar to that of Fox's rapid kick.

Many elements of Solid Snake are actually taken from Naked Snake (AKA Big Boss) in Metal Gear Solid 3.

Sometimes when Snake uses his C4, it is in the shape of a butterfly, an homage to Naked Snake shaping C3 into a butterfly before planting it onto a fuel tank in Metal Gear Solid 3: Snake Eater.

If the player does the down taunt command in a split second at Shadow Moses Island, the Codec will appear. One of three characters will appear (Colonel Roy Campbell, Hal Emmerich, or Mei-Ling) and give a short description of any random character on the battlefield.

Snake appears to dislike Sonic according to his Smash Taunt conversation with Otacon when battling the hedgehog. Whilst the reasons are mostly unclear, one popular theory is that it references how Snake's Japanese VA, Akio Otsuka, is the son of Chikao Otsuka, who voices Sonic's nemesis, Doctor Eggman/Robotnik. Coincidentally, Chikao also voiced Big Boss in the then-upcoming Metal Gear Solid 4: Guns of the Patriots. It's also possible Snake's disliking of Sonic is a reference to how hedgehogs eat snakes in the wild.

The reason that Snake was included in the game was to satisfy Hideo Kojima's son, who was a big fan of the series and wanted to see one of his father's characters in the game. Kojima was also hoping to expose younger players to the character as The Twin Snakes was the most recent Metal Gear game on a Nintendo platform. Kojima had also previously desired Snake to be in Super Smash Bros. Melee.

Sonic the Hedgehog in both Brawl and Ultimate can outrun the F-Zero vehicles on the Big Blue stage from Melee if he has the Bunny Hood equipped. This can also be done in Ultimate with any fighter who is faster than Greninja.

Both Ness and Lucas are unable to learn their Final Smashes (PK Starstorm) in their respective games. Instead, it's a move that both Poo (Ness' partner) and Kumatora (Lucas' partner) learn. In both Final Smash trophies in Super Smash Bros. Brawl, it says the partners taught them their respective moves so that they could use it in Brawl.

In the Port Town Aero Dive stage, there's a giant R.O.B. with glowing red eyes.