They never really explain how these supposedly extinct pokemon are just around. Chatot gets attacked by Fossil pokemon in Explorers, but they've said that some could still be around hiding in unexplored places. But then you also have pokemon like Archen who are part of an exploration guild and treated no differently than any other pokemon.

And Mystery Dungeon can't take place during prehistory because pokemon like Klinklang are around, so did the fossil pokemon just not go extinct and never change?

Can someone clear this up for me?