This actually happens quite a bit with teams to have at least two losses. Going undefeated or just one loss is rare. BYU going undefeated and the rest of the country not going undefeated is always the scenario to get in. But there are many one loss teams that would get in before an undefeated BYU (and some two loss teams). Hence our need to not have more than two one loss teams for us to get in.
Of course, all hypothetical. But if BYU is undefeated I have to believe all the other parts will fall in place.