This has happened twice to me. Once the conductor triple-punched the ticket because of the seating situation (lack of seat with a reserved seat). Once a customer service agent in WAS did so due to major service issues on the train I had just gotten off of.
To "redeem" the credit, I just had to go to a ticket counter. I was really skeptical the first time (I thought they were just pulling my leg to get rid of me), but I turned in the ticket stub and the agent deducted the amount of 50% of the triple-punched ticket from my new ticket. This was 5-6 years ago, and I remember thinking "What a strange way to do things!"