There's an easy explanation for that: the original Constitution, of course, didn't number the clauses. That's done later, for reference. The original Clause 3 was later superseded by the 12th Amendment. In versions of the Constitution you can find online, that clause is often highlighted somehow because of the change. So if you don't count Clause 3 (because it's been replaced), that makes the original Clause 5 now Clause 4.
Clear as mud.