It happens sometimes. However at the end of the season it shakes itself out usually. Early on you can have a 6-0 Big XII team not ranked (no AQ conference will ever have a team 6-0 IRL that is not ranked), but at the end of the season it gets sorted out.
The big glitch in poll logic is a 10-2 team can blow out the #1 team in the nation in the conference championship and leap from #7 to #2 and play for the NC over a 12-1, 11-1, or even a 12-0 team. (It happened once, but it was a non AQ that got leaped)