Top 10 Plot Holes in Nintendo Games (Counting Both First-Party and Third-Party Ones)

The items in this list have been selected by the author of the list for you to vote and comment on.
The Top Ten
1 None of the Zelda games (especially Breath Of The Wild) ever truly explain exactly where they are supposed to take place in the series' overarching alternate timelines
2 When the Shroobs take over the Past Mushroom Kingdom in Mario & Luigi: Partners In Time, the Present Mushroom Kingdom remains exactly the same, as if time itself considers it literally impossible for Mario and Luigi to not win the anti-Shroob war
3 Omega and Zeta Metroids are ridiculously larger in Another Metroid 2 Remake, Samus Returns and Metroid Fusion than they were in the original Metroid 2, and also no longer have the ability to fly
4 When Link deposits money into the Clock Town Bank and then rewinds time to back before he made his deposit in Legend Of Zelda: Majora's Mask, the money still remains in the bank
5 The layout and appearance of Planet Zebes (particularly Brinstar) changes SO much between Metroid: Zero Mission and Super Metroid that it makes the place look almost like an entirely different planet (no real explanation for this either)
6 The one and only official win on Glass Joe's non-Title-Defense career record in the Punch-Out series is said by the comics to have come from Little Mac, while Super Punch-Out leaves it up to you to guess whether it came from Gabby Jay or NICK BRUISER
7 The true final level of Cave Story (Sacred Grounds AKA Hell) actually DOESN'T feature an evacuation time limit, despite the fact that the entire floating island that the game takes place on is completely collapsing during said level
8 Mr. Sandman comes from Philadelphia in the arcade, NES and Wii versions of Punch-Out (the latter of which also makes him significantly lighter-skinned than the others) but is said to have come from New York in Super Punch-Out
9 Ganondorf is said to be the only non-female member of the Gerudo tribe in the Legend Of Zelda series
10 Super Punch-Out never actually explains whether its lead protagonist is supposed to be a much older and stronger Little Mac or just Mac's successor altogether (apparently, Nintendo says he's supposed to be the latter)