So every single Marowak mother in the world dies and every single Cubone in the world takes its skull and hides behind it, even when we have the mother accounted for, and no Cubone without skulls exist?
Relax. Not only have things like this been happening since the beginning, but there's remarkably little reason to care. It's just a unique bit of flavor; don't think about it too hard or care about it too much, because you're only ruining your own experience (and no, no one else is going to be impressed by the fact that you've pointed this out when obviously no one else has, nor enlightened by this new information because they didn't realize the contradiction, if that's what you're after).