Upvote:5
The bank has no way to know if you took the flight or not. They only know that the airline or Orbitz processed a charge for the flight. Likely the bank person you spoke to simply assumed that was the reason.
When you request a booking, the airline or Orbitz request authorization for an amount equal to the ticket price. This authorization is what the Orbitz agent mentioned would be "cancelled". It drops off automatically based on the card issuer's policy and could be anything from 48 hours to a month, unless the airline or Orbitz process the authorized charge.
In your case, it seems a glitch or human error caused the charge to be processed. Best guess, your booking was still active in the system and billed on the flight date (no shows are treated the same a folks who fly, the ticket value is "spent" or billed in your case).
The airline can check their system to find the charge and refund it (the paperwork you submitted). You can also file a chargeback with your card issuer but I would allow the airline a little time to sort it out before resorting to chargebacks.