I've had this happen with agents before, in 1K rooms or at check-in counters. When there is a delay, or a mistake. On a trip outbound, I checked my eupgrades and nothing was collected, on the way home, I saw the same agent, who sees me alot, and I asked him.
He said that he told the system he collected paper, rather than eupgrades.
Anyway, I've kept the details very ambigous to protect the innocent.
-A