*In HG/SS, Pokémon received as gifts from a Pokéwalker not registered to that game still count as yours in terms of OT and ID number. Meaning you could gift, for instance, a high-level Golbat from one of the later Pokéwalker courses to a game that hasn't even gotten to Violet City yet, and it'll obey without question.
*There was a period of time where a level 100 Arceus was distributed to B/W... through the Dream World. Since Entree Forest Pokémon count as catching wild Pokémon, that adds up to a potential level 100 with your Trainer ID as early as right after the first Gym.
*In Red and Blue, all of the attacks that were contained in the TMs Gym Leaders gave out could not be learned by leveling up at all. This changed in Yellow when Thunderbolt was added to Pikachu's level-up movepool.
*Flygon was supposedly meant to Mega Evolve, but didn't receive a Mega Evolution due to lack of good design ideas.
*Despite Weezing's decidedly asymmetrical appearance, its sprites still get flipped in any instance where one's sprite is to be flipped (such as contests), even though most other asymmetrical Pokémon, like the Budew line, wouldn't get their sprites flipped in the same situation. Weezing's ability to inflate and deflate its heads might explain this away, except this doesn't explain how the oval on the smaller head switches places with the larger head's skull and crossbones.
*Audino and Diancie are the only Pokémon from their respective generations to Mega Evolve. Coincidentally, both of their Mega Evolutions are Fairy-types.
*In the anime, assuming the animators did not take any liberties with the sizes, Jessie's Pumpkaboo is Super Size- it is consistently shown to be twice as large as James's Inkay, which fits with the heights of Inkay and Super Size Pumpkaboo- any other Pumpkaboo size is much closer to Inkay's height.
*The Park Ball from Pal Park is programmed into Generation VI's games, but is not actually usable in battle.
*Despite having higher Attack than Special Attack, Weezing has never had any physical Poison-type moves since before the physical/special split. It can't even learn Gunk Shot, despite the move fitting it beautifully.
*Koffing and Gastly could know Sludge Wave as a special move from the Dream World, and the Shiny event Gengar knows it as well, but the Koffing and Gastly lines cannot learn Sludge Wave from the TM. For some strange reason.
*The very first instance of a Pokémon in the anime using a move it doesn't actually get dates back to the second episode, where Samurai's Pinsir used Tackle. As time passed, these instances became less and less excusable, culminating in some of the latest mistakes, such as Gulpin with Water Gun and Slurpuff with Electro Ball.
*In the anime, even if they've been seen using it in their previous stage, no Butterfree, Beedrill, Beautifly, or Dustox has ever been seen using Harden.
*Despite its frequent appearances in Kanto, the Orange Islands, and Johto, Ash has never scanned a Weezing or an Arbok with his Pokédex. It also took him until Hoenn to scan Meowth, and even then, he believed that he was looking up a Kirlia which turned out to be Meowth in disguise.
*Despite the general stupidity of the games' average AI, any Trainer going back as early as Ruby and Sapphire will switch their Pokémon if they are facing a Shedinja and their current Pokémon can't do anything to it, but they have something else that can.
*Dedenne is the only Pikaclone whose Hidden Ability doesn't grant it immunity to Electric attacks.
*Reflect Type's effect is the same as Conversion had in Generation I.
*Psybeam, Psychic, and Hyper Beam currently have the same sound effects they had in Generation I (I sure wish they'd do that with Rock Slide as well).
*Despite the move seeing frequent use, Hidden Power's unique aspect of being a different type for each user has never been touched upon in the anime.
*Despite their evolutions not being introduced until Generation IV, Lickitung and Piloswine were able to fulfill the necessary conditions to evolve as early as Generation II (learning Rollout and Ancient Power, respectively). Despite this, Eevee evolving into Leafeon was made to depend on leveling up near a Moss Rock, instead of going for the obvious Leaf Stone.
*Lapras was only able to learn Solar Beam in Generation I.
*In Colosseum, Shadow Pokémon could be encountered Shiny, but were likely to become non-Shiny when Snagged, due to the game recalculating everything about them once they were caught. Conversely, non-Shiny Shadow Pokémon could turn Shiny once snagged. In XD, the issue was avoided by Shiny-locking all Shadow Pokémon. Poké Spot wild Pokémon, however, can still be Shiny (though I've yet to find a Shiny in Orre myself...).
*In Generation IV, if a wild Shiny broke out of a thrown ball, it would sparkle again. This feature was absent in all other generations (which is a shame- it could prove extremely useful if you missed the sparkles and have found a Shiny with an almost unnoticeable color difference, like Seel).
*In XD's Mt. Battle, one of the Trainers would say something about using the same combination of Pokémon as someone else, just before sending out a Cacnea and Chimecho, which matches the team James had in the anime at that time.
*In HG/SS, Biker Reese uses an Arbok in addition to his Weezing during rematches.
*Despite both Pokémon and move (as well as the TM containing said move) existing from the very start, Psyduck was unable to learn Psychic from a TM until Generation IV- it could learn it in Generations II and III, but only as an Egg move.