We fix wrong and nonsense things from the past generations (expecially the 1st) with X/Y pokédex descriptions or some other ways, I'll start:
>Cubone:
"for a modest period of time it was thought to wear its mother's skull. This is due to an old story happened in Kanto, where a Cubone was thought to have lost its mother. Actually its mother wasn't dead That means that Marowak gets a new evolution, very similar to marowak but ghost type like the one in my pic related, so in the new evolution's pokédex entry they will say that it was mistaken for a dead Marowak. Marowak evolves somehow when it has low HP now. and the "Skull" is in fact an exoskeleton."
>Voltorb/Electrode:
during some experiments on pokéballs in Kanto some Voltorbs came out from nowhere, so due to their resemblance with a pokéball the scientists thought that Voltorb was the result of their experiment on a pokéball. Actually it was later proved that some specimens of that pokémon also existed in the past. In fact Voltorb line exists in Oblivia's past.
>Clefairy:
Due to its affinity with the Moon and the moonstones, in the past some men thought that this pokémon came from the Moon. Now we know that the Moon is inhabitated and Clefairy is an Earthling-pokémon.
>Grimer and Muk:
It was thought in the past that Grimer was a pile of radioactive mud, but in fact it has a brain, a stomach, lungs and other organs and mud is just it's den. Some people saw Grimer came out from nowhere in mud so they thought that mud turned into Grimer, and so began the legend.