Earlier quoted context omitted.
This was decades ago, the ticket machines were not real-time connected to anything. It's entirely possible the numbers accounting used for ticket sales was the amount of cash retrieved from the machines, and there was no separate system keeping track of the tickets printed.
They likely counted the number of passengers via turnstiles or a gate or something. Think passenger count would be a good indicator of expected revenue and there would be a pretty clear gap. Probably one of the things the auditors noticed that was explained away by buggy code.
There is a pilot project[0] to put turnstiles/gates at two stations, but this is to keep the homeless out of the stations, not to count passengers.
[0] https://www.cbc.ca/news/canada/edmonton/transit-turnstiles-o...