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In Episode 70 of the anime Meowth is states that his species normally is quadruped and he had to learn to walk on twos. However, the games have always portrayed it being able to walk on twos. Later episodes of the anime, as well as Alolan Meowth, showing it can do this naturally.
Pokemon Sun and Moon game concept art has it kidnapping Ash and Serena from the Pokemon anime. This gag has never appeared in the games but has been a reoccurring gag in the anime, although, it targets the Team Rocket Trio rather than Ash and his friends.
Only 6 Pokemon have been in every single Regional Pokedex (Unless one were to count BW's Unova Pokedex as separate from B2W2's).
Porygon-Z and Porygon2 have also made cameos, but only as stock art in the Johto Pokerap and Kyurem VS. The Sword of Justice.
Diglett also learns Aerial Ace, a Flying-Type move that is often shown to be used in the air, with a Flyinium-Z it can use Supersonic Skystrike which also requires the air to be used. Dugtrio and Diglett are given a rock-like platform while performing this move.
Pikachu DS was a tech demo for the Nintendo DS shown off at E3 2004. It is based on Hey You, Pikachu! and Pokemon Channel, even using a similar Pikachu model. It's made to test the microphone and touch screen. Although unavailable, remains of it were used in Pokemon Dash.
Art of the Ultra Beasts' homeworlds from the Fall in the Ultra Beasts merchandise campaign. Each Ultra Beast got it's own artwork except for Poipole and Naganadel, which originate from Ultra Megalopolis. This is the only time Blacephalon and Stakataka's homeworlds have been seen.
According to Masahiro Sakurai, he new a Pokemon from X and Y would be added to Super Smash Bros. for 3DS/Wii U. This Pokemon in the end turned out to be Greninja and was decided before it even appeared in a Pokemon game. The developers only had concept art to rely on creating it.
In Pokemon X and Y, Gengar is the only Pokemon with the ability Levitate that is unable to be used in Sky Battles. This is likely due it's Mega Evolution being attached to the ground. Normal Gengar completely lost the ability Levitate in Gen 7 being replaced with Cursed Body.
Azurill has a different gender ratio than that of it's evolutions. Depending on it's personality value, 1/3 of female Azurill will evolve into a male Marill. This error was fixed in Generation 6 in X and Y, however, the different gender ratios remain present.