How to Fight A Citation?

I am a regular rider of Metrolink. When I was commuting to work on the weekends for the last 3 years, I have ridden Metrolink. When my brother needed to commute to school, I recommended Metrolink. And after my car was totaled, I found Metrolink to be a good option for my bi-weekly trips to visit doctors and to see my family. In the past, I have always punched my ticket without being prompted, but on this particular occasion, I was running late for the last train of the day. While I did not have time to punch my ticket, I was not worried because set precedent was that the conductor would write-in and manually punch the ticket. I had done this on one similar instance with absolutely no recourse. I had after all pre-paid for my ticket 10 p ticket. I was not evading fare. Today, however, the conductor wrote me a citation, despite the fact that I gave him the 10-fare p to validate. I called the Metrolink customer service line immediately and the gentleman calmly agreed that conductors have been known to manually validate tickets, despite the general protocol. When I rode Metrolink more often, I was familiar with my conductors and it was this friendliness that kept me a constant customer. Now not only do I face a citation of $250 on top of the $108 I already paid for my p. How do I go about fighting it? It doesn't seem fair that some conductors validate, while others write citations, ESPECIALLY since I had the ticket and asked him to validate it. Any insight would be welcome. I used to love Metrolink, especially with the high gas prices, but this whole incident leaves me pretty sore.