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I feel like the original Cubone and its dead mother was supposed to be a single one-off Pokemon and when they expanded it to a full species (2nd Gen bringing along breeding and all) they just never bothered thinking about the weird way the lore contradicts the games.
Either that or, as the beta Pokemon leaks confirmed was at least at one point the idea, all Cubones are orphaned Kangaskhan, meaning Marowaks are either not fully grown or stunted by not being adequately raised. Which begs the question of how male Cubones could exist in a purely female species, but whatever.
