Unfortunately, I don’t think this can really be explained in a manner that reconciles Pokedex entries and game or anime information. People have come up with many theories over the years, but none of them really works.
- Do female Marowak die after giving birth? But then there would probably end up being a lot more male Cubone than female. They have a 50/50 gender ratio. Besides, purely in terms of game mechanics, your Marowak don’t die if you breed them.
- Is Cubone an immature Kangaskhan? This is a theory that was brought up seriously by many players back in the day, but it doesn’t really make sense. It’s just pure speculation.
- Does Cubone kill its mother? This doesn’t really make sense, since the Pokedex says that Cubone is sad about her death.
Besides, all of these theories (and basically any other) suffer from the flaw of a replacement ratio: One can easily see that if every Cubone has its mother’s skull (and not its father’s) then there must be at best only one Cubone for each breeding pair. In other words, the ratio of Cubone to Marowak parents is no better than 1:2. This is below the viable replacement ratio for a population.
In my opinion, there’s really only one sensible explanation:
There are many signs that we shouldn’t take the Pokedex information from the games at face value.
For example, with respect to Marowak, Gold says:
It collects bones from an unknown place. A Marowak graveyard exists
somewhere in the world, rumors say.
However, Crystal presents the same information as fact:
Somewhere in the world is a cemetery just for Marowak. It gets its
bones from those graves.
This suggests that some Pokedex entries are presenting rumor as fact. There are many other examples where Pokedex entries just make no sense. For example, we are told that Banette used to be a plush doll:
A cursed energy permeated the stuffing of a discarded and forgotten
plush doll, giving it new life as Banette. The Pokémon’s energy would
escape if it were to ever open its mouth.
But how does this fit with its pre-evolution, Shuppet, which may have been a discarded puppet, but was certainly doesn’t look like a plush doll?
Fire Red tells us that:
It happened one morning - a boy with extrasensory powers awoke in bed
transformed into Kadabra.
But this same information is presented as rumor in Pokemon Sun:
A theory exists that this Pokémon was a young boy who couldn’t control
his psychic powers and ended up transformed into this Pokémon.
And of course, this all makes little sense when we consider that it evolves from Abra, so why would its origin be a little boy?
There are many other examples of Pokedex entries that make little sense, or outright contradict themselves or other Pokedex entries.
In the end, I think the most sensible thing to conclude is that the Pokedex is flawed. It incorporates myth and rumor as well as research, and sometimes (as the previous examples show) passes them off as fact.