This is not necessarily a bug, and maybe it's already documented somewhere. I've been confused several times by the differences in cloning logic:
Cloning a gameobject instance in scene adds a new Constant ID value to the clone, but cloning a prefab keeps a duplicate in on the copy.
So, if I ever want to clone prefabs with constant Id's, I probably want to throw them in a scene, clone them, and then drag into a new prefab file.
This might be intended behaviour, but as I've been wondering about this a longer time, I thought I'd just a discussion about this. "Works as intended" is a good enough answer

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