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.

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.

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.

There is evidence suggesting that Pikachu in this game is actually Pichu from Super Smash Bros. Melee, albeit evolved:

• Pikachu in Brawl uses Pichu's wall jump ability from Melee.
• Pikachu's Final Smash in Brawl is Volt Tackle, which, in the Pokemon games, can only be inherited by an egg-born Pichu.
• Pikachu's blue costume in Brawl uses the goggles worn by Pichu's blue costume in Melee.

Super Smash Bros. Brawl was originally planned as a launch title for the Wii, meant to showcase the difference between the Gamecube and the Wii (mainly via online capabilities), just as Super Smash Bros. Melee showcased FMV and graphical capabilities that the N64 was incapable of.

In the Japanese version, two games featured in the Nintendo Chronicle list are Jump Super Stars and Jump Ultimate Stars, a duology of Smash Bros.-styled fighting games released for the Nintendo DS that serve as crossovers between several Shonen Jump properties. Coincidentally, both games feature Goku from the Dragon Ball series, a highly-requested non-gaming character for the Smash Bros. series.

In 2023, a webpage on Nintendo of Japan's website was created to celebrate the 40th anniversary of the Family Computer. One of the subpages is a list of nearly every game published by Nintendo for the system, including those released exclusively for the Disk System peripheral. The only other known official list of Nintendo-published Famicom games available is the Chronicle in the Japanese version of Super Smash Bros. Brawl.

However, the Famicom 40th Anniversary subpage omits several games that were included in Brawl's Chronicle. These include:
• Popeye, as well as its spin-off titled Popeye no Eigo Asobi, likely due to licensing issues with King Features.
• Spartan X (released as Kung Fu outside of Japan), likely due to the game being a license, as it is based on the movie Wheels on Meals.
• Miho Nakayama's Tokimeki High School, likely due to the game heavily featuring real-life Japanese idol, Miho Nakayama.
• Ginga no Sannin, a port of the home computer game The Earth Fighter Rayieza by Enix. It is not known why this game was excluded from the list.
• All re-releases of standard Famicom games for the Disk System (such as Super Mario Bros., Tennis, and Mahjong). The Famicom cartridge re-release of The Legend of Zelda is also omitted.

In addition to these omissions, while the Chronicle lists Mike Tyson's Punch-Out!!, the Famicom 40th Anniversary subpage instead lists the original Gold Version released exclusively in Japan, which did not include Mike Tyson.

As of Super Smash Bros. Ultimate in 2018, only three characters that started out as Assist Trophies became playable in future installments:

•Little Mac, an Assist Trophy in Brawl, then became playable in Super Smash Bros. for 3DS/Wii U
•Dark Samus, an Assist Trophy in Super Smash Bros. for 3DS/Wii U, then became playable in Ultimate
•Isabelle, an Assist Trophy in Super Smash Bros. for 3DS/Wii U, then became playable in Ultimate.