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. 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 Wolf's death as he is by Falco's. Of course, in the games, Falco is one of Fox's closest friends, whereas Wolf alternates between being The Rival or Arch-Enemy to him.
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 Ganondorf. Said Bomb was used to kill Red. Since Ganondorf and Zelda are in cahoots, he was the one that had Red killed, simply because Red told him off in his first act of bravery.
Going back to Red's death, there was a justifiable reason for Ganondorf to have him killed. As Samus says herself, his house is the "safest place in the city with all those pocket monsters around". Red was sitting on a veritable army of super powered creatures, that could be used at any moment to threaten Ganondorf's power. And by standing up to Ganondorf, Red had just shown that he had a willingness to use them offensively, and was not the innocent, harmless, naive kid everyone thought he was, but, as Ganondorf himself pointed out, had the makings of a true hero, and it was the aforementioned misconception of Red that kept him alive as long as he was. Once he showed that he was dangerous, he had to die; knocking out his Pokemon as a healthy side effect.
Many of the Mythology Gags can be this if you think about the history of the games involved.
Here's one that can be made entirely by accident. Towards the end of the series, Kyle Hebert's beard became noticeably white, creating continuity errors. However, one could argue that Wario knows that the battle is coming and is gradually becoming more and more nervous.
When confronted in the alley way Luigi sees a baseball bat on the ground and uses it during the short battle. Soon after Lucas and Ness appear, the latter of whom isn't carrying around his trademark bat.
When Link talks to Luigi about Dedede's murder, he mentions that forensics found bits of skull like what would be the result of getting hit in the head with blunt force trauma. This doesn't get mentioned further, and Luigi notably leaves it out while trying to profile the killer, but remember, Ness uses a baseball bat...
This was an error on the part of The Escapist. The series had been allowed to not be censored, unlike most things uploaded there at that time, but that episode was the only one where the ball was dropped.