It appears that the Klutz ability prevents Lopunny's mega evolution, at least it does with the shiny one I have in my team, but I don't see why would the regular one work. No idea if you're taking any suggestions, but instead of making an exception for mega stones, I think Klutz should just be removed from all pokemon that have other options in the main series, it barely changes anything for wild pokemon and is purely detrimental for the player, especially if Buneary is chosen as one of the main characters.