* Ganondorf states there are some places he cannot go, then he later states no one can tell him where he can or can't go. [[spoiler:The one place he didn't go himself when he needed to is the place he knew the butchers would be, after he'd lost their trust.]]
* Fox is not anywhere near as broken up by [[spoiler: Wolf's death]] as he is by [[spoiler: Falco's]]. Of course, in the games, [[spoiler: Falco]] is one of Fox's closest friends, whereas [[spoiler: Wolf]] alternates between being TheRival or ArchEnemy to him.
* [[spoiler: When Kirby and Meta Knight square off during the jailbreak, the scuffle ends with Wario reporting that Kirby is dead, and all that was found was his burnt carcass, along with a... fire flower. The one Mario used to break into the cells. Knowing that Kirby used Meta Knight's armor to disguise himself, the question becomes how Kirby, alone with Meta Knight, could have burned him. The answer is simple: one of Kirby's powers in the later games was to gain new powers by devouring different items. He got his hands on the fire flower and used it to torch Meta Knight.]]
* If you pay close attention, you can see Zelda handing Wario the Pikmin Bomb, Luigi delivered to [[spoiler: Ganondorf.]] Said Bomb was used to [[spoiler: kill Red.]] Since [[spoiler: Ganondorf and Zelda are in cahoots,]] he was the one that had [[spoiler: Red killed, simply because Red told him off in his first act of bravery.]]