Okay, since another question similar to this was asked, I'll just copy-paste my answer here.
How could the Cubone possibly wear the skull if the skull is impossible to take off?
This one is actually quite simple, and is an example of animal decomposition. This takes place in 5 stages, named fresh, bloat, active decay, advanced decay, and remains. Let's go through this fun process! The first three stages have nothing to do with bone, but eat away at skin. By the fourth stage, the skull is revealed and Cubone puts it on its head. (since it's always at its mother's death) Due to the skull actually getting smaller in the fifth stage due to exposure, the Cubone cannot take it off, but it miraculously doesn't suffocate.
How could the Cubone possibly wear the skull if the mother is a Ditto?
Wild Cubone don't live in the same areas as Ditto. Cubone lives in mountains, while Ditto lives near people. This means they don't naturally breed, therefore making the mother always be a Marowak. If a Cubone's mother is Ditto, that means it either:
A) Wears a skull from a wild Marowak with no children to take it's skull
B) Wears a transformed Ditto's skull
C) Wears it's fathers skull
D) Obtains the skull through other means
How could the Cubone possibly wear the skull if the skull if the father is alive and well.
Same four options:
A) Wears a skull from a wild Marowak with no children to take it's skull
B) Wears a transformed Ditto's skull
C) Wears it's mother's skull (Assuming it actually had a mother and she is dead)
D) Obtains the skull through other means
Sources are in the above links.
