I thought that the humans here would always have bonded with Pokémon.

Maybe Archen had a lot of predators when they were alive, so her instincts are that everyone is an enemy. Even though she's a bird she doesn't seem to be able to fly, so she wouldn't be able to escape as easily and would need to be able to fight right from birth. Though even without flying she can run really fast. I'll have to try and ask her once she's more used to me.