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I solved it
Marowak dies when each cubone offspring hatches.
Cubone sees its mother's dead corpse, takes its skull and then marowak resurrects and regenerates a new skull. Cubone gets a skull and marowak lives once more. Cubone is traumatized by this and still cries.
This makes the pokedex entry correct. Cubone lost its mum and while it's mum is alive it's bot the same one.
Weirder shit has happened in pokemon so this isn't that strange.
