Partly inspired by this question.
I was originally thinking of asking, "What if a Cubone's parents are a male Marowak and a Ditto", but to be honest I'm not even sure if that's answerable, especially given that in-game a Cubone hatches already wearing said skull and your female Marowak never dies for it.
However, whilst thinking about that, I realised something.
When breeding a Pokemon with a Ditto, it is always the partner's species that is passed down, even if the partner is male. Therefore, in the case of Male Marowak X Ditto, you will end up with a Cubone egg.
In addition, Ditto cannot breed with itself. It simply doesn't work. Pokemon Moon explains this with its Pokedex entry for Ditto, stating it "Doesn't get along well with its fellow Ditto".
There's a fan theory not yet confirmed by Game Freak or Nintendo that Ditto is actually created by humans as prototype clones of Mew, before they perfected Mewtwo. But even if that were the case, there'd still only be a small and finite number of Ditto around, limited to specific lands, but there are plenty of Ditto in some areas of the Pokemon world, including some where you wouldn't expect to find them at all, like the Desert Underpass in Hoenn, or Mount Hokulani in Alola.
All in all, given that Ditto can't breed and there's been no confirmation that I can find of them having been created, where the heck do Ditto come from?