Here are a few created by generational differences that I'm amazed I didn't see mentioned:
1)If Mew is the ancestor of all Pokémon, then how could the universe have started with Arceus?
2) Cubone's Pokédex entry (I'm not sure in which game though...) says something about it being abandoned after birth (I think) well Pokémon aren't born at all! They're HATCHED!
Hora kimi no sugu me no mae ni iru, sono namae wo saa, itte goran kono boku no namae wo! eFTo
In a book in the Canalave libray it says: once there was nothing, just chaos. In the centre of this chaos, where all things become one..... Wait, how can all things become one when there is nothing there.