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Pokemon is an ever-expanding franchise, adding more games, characters, types, regions, and especially more lovable, tough creatures known as Pokemon. With this endlessly expanding lore and even remakes of games that were originally released years prior, there are bound to be retcons in certain lore decisions that were made earlier in the series.
Pokemon isn't generally a series that frequently contradicts itself, it has a very linear, straightforward concept and builds upon it mainly by expanding the world. With every new region, there are new characters, creatures, and lore that are exclusive to that region in the world of Pokemon. However, with the series running for nearly thirty years, there are a handful of retcons that have been built up with each new addition to the world of Pokemon.
6 The Pokemon World Is No Longer Part Of The Real World
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Pokemon Red, Blue, and Yellow made it clear that the world of Pokemon was an extension of the real world. There have been plenty of regions heavily inspired by or based on real places, but the Kanto region was made as a fictitious representation of the real-life Kanto in Japan. This is clear from the many references to real-world concepts such as war, religion, countries, and animals scattered throughout the games.
Slowly, these real-world references have been taken away, likely due to the fact that expanding the world of Pokemon while also keeping the canon that it's a part of the real world is a difficult box to have the franchise stay inside. These changes have included Parasect's Pokemon Stadium Pokedex entry being changed from saying that its "spores are sometimes used as medicine in China," and Vermillion City's Lt. Surge no longer being American.
5 New Pokemon Types Just Exist
With every new mechanic in the games, there's generally a lore explanation behind it. Such as ride Pokemon being exclusive to Alola, Wishing Stars powering the energy used for Dynamaxing in Pokemon Sword & Shield, and the Mega Stones being created by the energy emitted by the Legendary Pokemon Yveltal and Xerneas in Kalos.
However, there is never any lore explanation as to why new Pokemon types are added. They simply just appear, changing the types of Pokemon that previously only had one type, such as Magnemite becoming an electric/steel-type after the inclusion of dark and steel types in Pokemon Gold & Silver, and the Ralts and Mime Jr. evolution lines becoming psychic/fairy-type after the fairy typing was introduced in Pokemon X & Y. The lore behind new types and the changes in other Pokemon types has never been fleshed out, mostly just brushed off with the comment of new discoveries being made all the time.
4 Oak Lied About The Pokedex
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It's become canon as of the release of Pokemon Legends Arceus that Professor Oak is a liar. In Pokemon Legends Arceus, which canonically pre-dates the events of Pokemon Red & Blue by centuries, Professor Laventon introduces the player to his invention and passion project: The Pokedex.
Professor Oak notably takes the credit for inventing the Pokedex when the player first meets him in Generation I. Since it's clear that the Pokedex was an idea that pre-dated the existence of Professor Oak, it's a bit strange that he confidently takes the credit for inventing the Pokedex when it's now been revealed that it was created long before the events of Pokemon Red & Blue.
3 Sinnoh Turned Hisui
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Although the lore in Pokemon Diamond, Pearl, and Platinum wasn't as fleshed out as players would've liked, it was never stated that the region of Sinnoh had gone by a different name in the past. When it was revealed in Pokemon Legends Arceus that the Sinnoh region had been named Hisui centuries before the events of Pokemon Diamond, Pearl, and Platinum, it left players a bit confused.
Not to mention that "Sinnoh" refers to a deity rather than a region throughout Pokemon Legends Arceus. The re-naming of the region in the past and the switch from Sinnoh being referred to as the name of a deity rather than the region itself is considered a huge recent lore retcon in the franchise.
2 Real-World References In Pokedex Entries
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The real-world references in the world of Pokemon have dwindled over the years. While there were a handful of references placed in the dialogue between NPCs and characters, many of the real-world references came from entries in the Pokedex from Generation I.
Raichu's Pokedex entry used to state that it was strong enough to electrocute an Indian Elephant, but has since been changed to say that it can take down a Copperajah. Similarly, Ponyta's Pokedex entries in Pokemon Stadium and Pokemon FireRed claim that it can clear the Eiffel Tower and Ayers Rock, respectively, in one leap. Legendary Pokemon have had real-world references tied to them as well, as Mew is stated to have been originally found in the jungles of the South American country Guyana.
1 Giovanni's Return In Gen II
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After Giovanni, the ring-leader of the evil organization Team Rocket, is defeated by the protagonist in Pokemon Red & Blue, he disbands Team Rocket and makes a turn for the better in deciding to dedicate his life to studying Pokemon. One of the biggest plot points of Pokemon Gold & Silver, as well as Pokemon HeartGold & SoulSilver, is the remnants of Team Rocket attempting to contact their old leader once again.
Canonically, these messages turn up nothing, as Giovanni never responds or returns to aid Team Rocket. However, an event in Pokemon HeartGold & SoulSilver confirms that Giovanni did hear Team Rocket's radio broadcasts attempting to contact him, but never returned due to being defeated by the protagonist. During the development of the original Pokemon Gold & Silver, there were plans to give Giovanni a proper return outside of an event planted in the remakes. Originally, he was conceptualized as a member of the Gen II Elite Four, and his sprite could even be found in the Radio Tower, implying that he would've responded to Team Rocket's messages in one way or another.