Let's say that there is a good witch and an evil clone of that witch...do they count as the same witch or different witches for the purpose of determining if people can be affected by a hex multiple times in a 24 hour period?
Well, the Clone spell says "treat the clone as if it were the original character raised from the dead". Which would lean toward the side of "same witch" for the hex limit.
However, the Clone spell can't make an active clone while the original is still alive.
So my answer would depend partially on how the evil clone was made, but since the clone is now possessed of a different morality and goals (differing alignment) it would point to the idea they should be treated as different individuals now.
Older edition Clone spell descriptions had some text about clones created while a caster was alive, but PF Clone is basically just Raise Dead.
Lets change the idea from clone to simulacrum. Now what?