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Everything having to do with Kangaskhan and Cubone.
The weirdness comes mostly from them being designed before breeding was implemented, but it’s very odd that Kangaskhan comes out of the egg with a child already in its pouch and Cubone comes out of the egg with its mother’s skull already on its head.
Here’s what they could have done: make the baby Kangaskhan its own Pokemon, then have it evolve into Kangaskhan unless it’s holding a Skull item, in which case it will evolve into Cubone and then Marowak.
There would still be the mystery of what Cubone’s face looks like since he’d be a different Pokemon than the baby Kangaskhan.