my student loan at Navient

I am writing this to dispute a 90 day late notice on my credit report involving my student loan at Navient. On January 16, 2013 I was informed by a Sallie Mae’s employee that on January 6, 2011 I had a $2.54 late fee on my student loan. I was then told that in that same month I had made two payments for $140.00. I was also informed that on March 14, 2011 there was another late fee for $1.28 and on March 23, 2011 a payment for $74.00 dollars was received. I am not understanding how can there be late fees when adequate payments was received to cover the late fee amount within the same month? Then to report a 90 day delinquent status to the credit bureau? I am paying one flat fee for ALL of my student loans and the other accounts are showing in good standing on my credit report. Even if I did not pay the late fee on the day it was due, when I made a payment it was not 90 day later.