One of the battle bonuses is called 'Switzerland', and is worth 12,00 points. It is obtained by not attacking (including missing) and not being attacked. This is a reference to Switzerland's neutrality during both World Wars.

There are six "unused" entries in the debug menu's level select for Versus matches. While most of them crash the game, only two of them work properly. The first one, TEST, is a large terrain test stage with a unique backdrop. The background comes from a coffee shop in Palo Atlo, California. The second one, TSEAK, is a test stage for "Break the Targets" and was reserved for Sheik.

In the background of the trophy room, several Nintendo consoles can be seen. The room includes a Nintendo 64 with the original Smash Bros. inside, a Nintendo Power with Super Smash Bros. on the cover, an NES, a SNES, and several other objects. If the language setting is switched to Japanese, the NES and SNES change to their Japanese equivalents, a Famicom and Super Famicom, and a Virtual Boy will appear next to the sunflower.

The Helirin is incorrectly named the Heririn. This was fixed in the PAL version.

Early English releases of the game changed the "Magnum Killer" (The Japanese name for Banzai Bill) trophy to "Bullet Bill", accordingly changing the game data to "Super Mario Bros. 10/85". The description acknowledges that that all the "Bullet Bills" in Melee are the rarer, extra-large variety, yet it seems the translators were unaware that those are called Banzai Bill. Later English releases fixed the name and description, but did not change the game data back to Super Mario World.

The Metroid trophies claim that the original Metroid was released in 1989 (8/89), but it was released in 1986.

The Great Fox trophy says that it first appeared in Star Fox, but its debut was actually in Star Fox 64.

The original boxart did not feature Link or Pikachu, and instead featured Mario being attacked by Bowser's Fire Breath move.

On the description of the Meta Knight trophy, it states that he made his debut in Kirby Super Star. This however is incorrect, as his first appearance was in Kirby's Adventure, four games before Kirby Super Star was released.

The Pokemon, Ditto, was meant to be a possible helper when a Pokeball was thrown. He was supposed to transform into the player that threw the ball and would help fight. However, there were problems with its programming and it was removed. By using an action replay, Ditto can be put back into the game, but he is lacking his "transform" ability. Instead, all it does is say "Meta!" (it's Japanese name being Metamon) and disappears. Anyone who runs into it is dealt 7-8% damage.

Captain Falcons' red costume was originally planned to say "Hell Hawk" on the back.

The Metroid trophy has an image reflecting off of its shell. The image is of the space station from the beginning of Super Metroid.

Luigi's voice is just a pitch-altered version of Mario's.

In Captain Falcon's "break the target" room, a picture of dolphins can be found on the left-most wall. This may be a reference to the original codename of the Gamecube, which was "The Dolphin".

In Luigi's "Break the Targets" room, the small square in the middle of the stage, which he begins standing on, is actually a Nintendo Gamecube.

There's a reflection of the 'Yoshi's Island' stage on the Metal Mario trophy.

There is a glitch that allows the game to advance to the stage selection screen without properly configuring the match. Any player that does not select a character will be set to Master Hand as a default. However, Master Hand will only respond to controller port 3.

An Excitebike racer from the game Excitebike, Balloon Fighter from the game Balloon Fight, Urban Champion from Urban Champion and Bubbles from Clu Clu Land were considered for characters that could be used to represent the NES era of Nintendo in the game, but Sakurai decided that the Ice Climbers would be far more fitting as fighters.

The Letters "2L84ME" (too late for me) are printed on the back of the Barrel Cannon Trophy.

Unused character intro loading screens for All-Star mode can be found by using the game's debug mode. They were most likely removed because the player may fight multiple opponents simultaneously in some rounds.