Not the same circumstances, but I had a website glitch last week when buying a ticket and selecting the upgrade with miles option. The site gave me a great offer to use miles to upgrade each way. I selected it during the checkout and it even let me pick first class seats. I then hit purchase and when the ticket issued I was back in main cabin, but DL.com took my miles!
Call to the Medallion desk and they couldn't figure out what happened. They cancelled the ticket and refunded my miles and I rebooked. Second time it worked. Agents can't see the "upgrade" offers given to you on the website. To them it appeared I used "pay with miles" to reduce the cost of my ticket.
Long story short, I just today got a call from DL offering me an apology because they forgot to actually issue the refund to my CC.