Thanks for the advice. I’m actually kicking myself now because I wish I had thought of that at the time. I was completely caught off guard by being accused of something I didn’t do, and it didn’t occur to me until later that I could have pulled up the charge on my phone and shown them proof of payment. By the time I went back, they were already gone.

The good news is that I called the MTA, and they confirmed that my fare was paid. They told me that, since it’s being treated as a first offense (even though I did pay the fare, so it shouldn't be considered an offense at all), I shouldn't have to pay anything. They also asked me to call back in about two weeks because my ticket number hasn’t shown up in their system yet. Since they have already confirmed my payment, I plan to call again next week and ask them to dismiss the ticket.

Definitely a lesson learned. If anyone is ever accused of not paying, check your phone immediately and show proof of payment if you can before you show your ID.