My favorite story happened to me about 2 years ago at JFK:
Was flying JFK-ATL-GIG LIM-ATL-JFK. Paid M fare both ways with upgrades. For whatever reason, when I went to check in at JFK they asked me to present the original CC used for purchase. Well, you see, that original CC was lost a month prior and I explained this to the agent. She then made a phone call and said she would put the new CC in the reservation as a notation. Something told me to MAKE SURE she was not going to charge my CC again, even though I felt a bit paranoid asking. The agent assured me all was good and off I went.
Fast forward 5 days later and I am sitting in my room at the Park Hyatt EZE when low and behold I see a SECOND charge for well over $2,000 on my new credit card. Before calling DL, that same little itch told me to check Delta.com and look at my e-credits. Well, guess what? I had an E-credit in the amount of the original ticket minus the change fee.

Furious, I called DL.
To make a long story short, the agent in JFK took it upon herself to cancel my original ticket and just give me an ecredit and WITHOUT authorization of any kind charged my new CC the price of the new ticket (essentially taking $4,400+ out of pocket instead of $2,200). I was so furious (but remained calm to the specific agent as it was not HIS fault) that the agent processed a full refund for the original ticket, booked me in full fare J on the return, gave me my certificate back, and gave me a $200 voucher for future travel.
Be careful with DL agents.