I had two similar situations happen to me (both in my favor). After 6 yrs on a 30 year loan I went to refinance, thinking I knew the balance on the loan. To my surprise it was $5k less. A printout of the history showed a $5,000 payment on 12/31 of year 2. I told them that I'd never made any extra payments. They didn't seem to care.
Last year I purchased some furniture and put it on my MC. My statement never showed the charge. I went back to the furniture store and they claimed I didn't owe any monies and never had a dispute with MC. To date, I have not had either party contact me about the dispute.