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Dr. Maddiman's Animal Experiment Yo-kai are named Squirty, Warty, and Blaster. This is a reference to the Pokémon evolution line of Squirtle, Wartortle, and Blastoise.
Untidy has the highest STR stat of all Yo-kai in Yo-kai Watch 2, before bonuses such as Yo-formance.
Unlike Everfore, Eterna does not have a pre-evolution except in episode 206 of the Yo-kai Watch anime, where she devolves into an unnamed variant of Grumples with blue bags under her eyes, purple shaded skin and cloak, and a yellow band around her waist.
Kuruhoshi Nayu and Elna Amami/Elzemekia are voiced by P Maru-sama, a popular Japanese YouTuber and singer known for their animated comedy skits.
Shien gets support from Thurston and Tengulightened in his Kourin Battle in Yo-kai Watch World. This is a reference to the movie Yo-kai Watch Forever Friends, where Shien has Shuten Douji and Karasu Tengu as his henchmen.
The Unchikumars from Y School Heroes episode 15's name is a reference to Poofessor's Japanese name, Unchikuma. It is also most likely a hint as to who Kumako, the creator of the Unchikumars, is reincarnated from, that also being Poofessor.
Komasan and Komajiro are completely separate beings from Shadowside Komasan and Komajiro, despite their identical names and similar appearances.
Bousou Rinne is the first "Rampage" Yo-kai to make a cameo in the non-mobile games, where he appears as a costume for the player to wear in Y School Heroes: Bustlin' School Life.
Although Thurston and Shuten Douji both have the same name in Japanese, and are based on the same real life youkai (also called Shuten Douji), there is no confirmation on whether they are the same being.
Including mobile games, more than 200 "nyan" Yo-kai exist in the whole franchise.