Yuji Naka said that Sonic the Hedgehog was originally set to appear in this game but couldn't be added in time. Sonic did make it into the followup game Super Smash Bros. Brawl (2008).
The intro movie shows Samus using a Missile against Ridely. Since the Samus's portion of the intro is based on Super Metroid, she wouldn't have Missiles at that point in the game.
Ness refers to his magic attacks as "PK" attacks. This is supposed to be "PSI." (The Earthbound games use the term PSI to refer to magic, though an early beta version of the game used PK, and this is probably what caused the error.)