I am surprised. I have perfect credit, bills paid on time... Once or twice due to life I have missed a payment and called when I found out. Bank Of America, Discover, and I think Citi bank have credited and no late payment was documented. One, I am not sure Citi or Discover said no on the phone, I wrote a letter and the credit was posted.
My suggestion would be to write a letter and request the late fee be reversed.