At best they are clumsily expressed. They aren’t natural (because what you’ve said is not very clear). There is probably a better way of expressing each, but without knowing your exact meaning it’s not possible to say with accuracy what a better option would be
I suspect you mean this for number 1:
There are two sets (of keys), each containing three keys, two of which are identical.
and this for 2:
The sets (of keys) each comprise three keys.
While 3 is more complicated to work out, but you might mean:
There are five keys on a set, which comprises two different pairs of identical keys and one other key.
4) should probably simply be:
The keys don’t match.