Pope Stephen II dies just a couple of days after his election. He was a popular candidate and elected unanimously, but because he dies before his consecration there's debate about whether his papacy was ever entirely official. In fact, he didn't even live long enough to be ordained a bishop.
This pope is listed officially as Pope Stephen II until the Second Vatican Council, at which time it's decided that he was never technically pope at all. Every pope after him who's named Stephen - which includes the one elected to replace him - now gets dual numbering.
Thus his immediate successor is originally listed as Pope Stephen III, but then gets listed as Pope Stephen II (III).