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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?

DisturbedNeo
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    Male and female hamsters hate each others guts until the female comes into season, they mate, then they start hating each others guts again. – Valorum May 15 '17 at 16:22
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    That's true, though in Pokemon breeding the chances of getting an egg are directly proportional to how well the two Pokemon get along in the Daycare. If two Pokemon "don't seem to like playing together", your chances of getting an egg is 0%, though it has to be said you only get that message when the two Pokemon are different egg groups or the same gender. – DisturbedNeo May 15 '17 at 16:46
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    Since they're basically blobs, perhaps they can reproduce asexually by dividing into two entities? Just guessing here. – tobiasvl May 15 '17 at 17:40
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    The way I heard it, the theory was that Ditto were Mew that used Transform so much that they lost their base forms. That would help explain why they're found everywhere, but not why there are so darn many of them. – jwodder May 15 '17 at 23:03
  • Now this is a good question: I was thinking the same thing! If you don't intend to accept Zephyr's answer, I'll try to find some sources to answer this. – Voronwé May 22 '17 at 13:44

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Some Pokemon are capable of reproducing in different methods than the traditional breeding mechanic presented in the Pokemon games. One example of this is another amorphous Pokemon, Grimer. According to it's Pokedex entry from Pokemon Stadium 2:

As it moves, it loses bits of its body from which new Grimer emerge. This worsens the stench around it.

This is a distinct method of asexual reproduction from the sexual reproduction which occurs in gameplay. So although Ditto might not be capable of breeding, it may have another method of reproduction.

Another thing to mention is that Ditto is considered an "urban" Pokemon, a pokemon which exists primarily coexisting with human civilization. As with some other examples, such as Grimer and Porygon, this may point to Ditto being a species created artficially, either intentionally or by accident. In this case, Ditto would not necessarily require a method of reproduction, if they are produced from some external process.

Zephyr
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