If what you were told was true, I bet the reservation was indeed cancelled before your arrival (for whatever bizarre reason) and the front desk resurrected it while you were standing there and assigned some random rate to it which differed from your confirmation. It is a CY after all...

Sounds like all is going to work out so don't condemn a entire chain because of it, I've had my share of minor billing issues at CY, SHS & RI over the years and they are always caused by some clerk at the local property.