Virgin Media's billing system

Just renewed my phone line rental saver. Got various acknowledgements from them, so far so good.
Received new bill from them yesterday. On in is recorded payment by card for Line Rental saver, payment of it AND a payment for the monthly rental

Phone them up and guy says oh I note we forgot to set the marker to say you've paid it.
Why if the billing system knows you paid does it insist on a separate marker being set?