Odd. You should be allowed to have both a vendor and an employee (or two employees) with the same SSN if you really want to. These are all valid cases.
And in any case, if the message says you have another employee with the same SSN and you don't, then the message is clearly wrong.
If you are blocked by QB and if you still have the vendor record with the SSN, what happens if you remove the SSN from the vendor?