Exempt employee and making up missed time

I am an exempt employee for a municipality. One morning I had car trouble and was an hour late for work. I did call work and explain the situation. Later the same day, my supervisor told me to just work an hour later to make up the time. The next day he presented me with a disciplinary letter for "excessive tardiness."-this was the first time I had been tardy since I don't remember when. I asked him how one instance could be excessive, and he said he had heard that I am late all the time. I asked him to look at my time card and give me the dates I was late (there are none.). He refused, saying he just was doing what he had to do. Is this legal? Note: I was on intermittent FMLA at the time and he gave me a very poor evaluation, citing that I was absent all the time. I used 3 sick days in 7 months, the rest of the time was FMLA. He was using that information for my "excessive tardiness".