There's a lot of theories about Cubone's mother, here's the two most popular theory that I've just found:
1. The Kangaskhan theory mentioned before. According to the Pokédex, Kangaskhans are so aggressive pokémon that they protect they children at even the cost of their lives. If this happens, the baby can not overcome this trauma, so it takes the last things remaing from her: the skull and the bone, and when it grows up, becomes a Marowak. That's also proven by the fact that in the 7 gen games, where the S.O.S. encounter mechanincs debuted, Cubones usually call another Cubone for help, but occasionally a Kangaskhan appears.
2. Cubone is an orphan Charmander. The flame on the tip of Charmander's tail is blown by an adult Charizard when the egg hatches. As seen in the anime, Charizards are extremely aggressive creatures, attacking the stronger or even type advantegeous pokémon recklessly, providing a huge chance for the mother Charizard's death. When the baby hatches, it can't develop a Charizard's most basic organs, like the wings without the tail flame, so it stays on the ground (at this point, we can regard that Cubone's and Marowak's Ground type is symbolical :D), and similarly to the Kangaskhan theory, it takes its mother's bones, and evolves into a Marowak when it grows up. This theory is also valid if the mother Charizard is alive, but refuses to raise the weak-looking hatchling. The disinherited baby sadly goes into the Charizard graveyard, where it finds an other dead Charizard's bones, and also turns into a Marowak when it grows up. This theory is proven by the similar shape of Cubone's bone helmet and Charizard's skull (it also applies for the Kangaskhan theory), and the pointed buds on Cubone's back, wich probably were developing wings, and wich only disappears when it evolves.
