In New Super Mario Bros., the Mega Mushroom actually has a size modifier applied to it at runtime to make its model smaller than the size at which it was originally designed.
Above is what the Mega Mushroom looks like when it is allowed to spawn without size modifiers. It is likely that this was changed during development since although it does make the item look very impressive, the ability to spawn it anywhere from storage would make it get stuck on most course geometry at that size.
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In Super Mario World, the floor of the boss battle rooms of Bowser, Reznor, Morton, Roy and Ludwig is made out of invisible Empty Blocks, while the visual tiles representing the floor do not themselves have collision.
In other words, the floor Mario appears to be standing on is actually a fake illusory floor he would fall through, and he is actually standing on an invisible floor made out of Empty Blocks. This can be seen in action by using cheats to spawn a P-Switch inside these rooms, which turns the Empty Blocks into coins and makes Mario fall through.
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Unused and mostly untextured models of Mario and Wario on scooters, found in the files of the Scooter Pursuit minigame in Mario Party 8. These were likely used at some point early in development for testing.
Note that Wario is standing backwards on his scooter, assuming a pose as though he is gripping the handles while the handles are actually behind him.
While this is most likely simply a side effect of the placeholder nature of the models, it is interesting to imagine that this could have been a quirk the developers wanted Wario to display in the finished game, whereby he would stand backwards on his scooter for humorous effect.
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Top: in the beginning of the intro of the Adventures of Super Mario Bros. 3 cartoon series, the Mario Bros. Plumbing building is seen from outside for a few frames.
Bottom: the background is actually a redrawn version of a background from the earlier Super Mario Bros. Super Show cartoon series, where it was a business with signs reading “FIZ” and “CYRO’S”. While this is likely merely a reuse of a basic concept to expedite the production, one possible in-universe implication is that Fiz/Cyro’s went out of business, and the Mario Bros. moved into that building.
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In Super Mario Sunshine, an audio glitch occurs if the map screen is opened on a specific frame after dealing the final hit to the Wiggler boss in Gelato Beach. The music will sound high-pitched and distorted, as heard in this post.
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Audio message of Mario talking about Super Mario Sunshine, found on Nintendo of Europe’s official site for the game in 2002.
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In Super Mario Maker 2, creating the contraption shown in the footage in the Super Mario 3D World game style and collecting a Super Bell while holding a trampoline and entering a pipe will cause the player character to enter the pipe internally, but not actually follow the pipe physically.
Instead, the character will ascend toward the top of the screen in the manner shown in the footage before the screen fades out (note that the Glory ray of light effect was added by the course designer to underscore the glitch).
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In Boulder Bowl Galaxy in Super Mario Galaxy 2, the “C'mere, Goomba” mission consists of luring a Goomba to a Gold Gearmo NPC who rewards Mario with a Power Star for this.
However, if the Goomba is lured to the Gearmo before talking to it for the first time, and is on the boundary of the goal zone when the task starts, the game will try to start and end the mission simultaneously. This causes everything except the Gearmo to freeze forever, requiring the game to be reset.
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Top: it is well known that the 1987 “How to Win at Super Mario Bros” guide published in the US used a unique design for Peach in its introductory segment where she herself has been interpreted as a Toad.
Bottom: the drawings actually originate from a 1985 issue of the Japanese Family Computer Magazine, which also contains this panel that was not included in the English guide. It appears that the comic was drawn at a point where not all information about the game was publicly known or even finalized, so the design for Peach was extrapolated from the design for the Toads.
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