They'll probably make you pay at the check-in desk. I got caught out by this last year. I'd paid the £20 by credit card when booked the upgrade, but it wasn't showing on the booking for some reason. I got there as the check-in was opening, but was then sent back to the ticket counter to sort out the payment. I then had to go the back of the check-in queue again Fortunately, there weren't that many people there, so it didn't take to long.

The check-in agent then tried to make me go back again, as the payment was still not showing. When he saw the angry look on my face, he jumped from behind the counter, ran over to the ticket counter and checked himself. He then checked me in

Cheers,
Rick