In regards to the nidorina and nidoqueen thing and the cubone thing, I’m going to connect them into a theory that makes sense. Cubone and Marowak were meant to be unable to breed, and gamefreak accidentally somehow put the unbreedable trait on nidorina and nidoqueen instead, and they never corrected their mistake by making nidoqueens able to lay eggs and marowaks unable to.
A lovely idea, marred only by the lack of any evidence whatsoever…
The story of Red and Blue establishes that a Marowak can be a “mother,” regardless of whatever else is going on with the Cubone skulls, so why would they have intended to make Cubone and Marowak unbreedable? Moreover, it makes perfect sense that, if they were going to make a mistake with the breeding rules, it would happen to a Pokémon whose relationship to gender is unusual – there’s no need to bring Cubone and Marowak into the picture to explain the slip-up with Nidorina and Nidoqueen, particularly as the two Pokémon have nothing to do with each other.
Pokémaniacal 