Fighting a dispute on credit report

Fighting a dispute on credit report

I pay my car payment online and have for two years now. In Dec instead of paying 297, I paid 287 on accident. After 90 days I got a "final notice" in the mail despite not receiving any other late notices. The note said I owed nearly $400 due to the late fees! I called, I got a rep who said it was because I was $10 short. She took my payment of the $10 and said that covered it and there would be no late fees. I asked if it show up on my credit as being 90 days delinquent. She said no. I checked my credit report yesterday. It shows up as me being 90 days. I have a very low credit score as it is. I'm not in debt, the only thing I owe is my car. The fact that I only owe on a car is the reason for my low score. What is the easiest way to go about challenging this, and do I stand a fighting chance of it getting removed?
Garden Update

Garden Update

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Three unknown trees with berries