Usually, when a booking is completed up to the payment stage, a PNR is completed and the seats are taken away from the inventory. They can remain so for 24 hours. Hence, you might have "booked" 2x2 seats, emptied the cheap fare bucket and the next booking has to be dne in a higher bucket. Just a guess, but that happened to me before.

The payment system is different from the booking system. I have seen it bug on quite a few airlines.