Having your books off by a few percent is indeed quite common. However, missing 20% on your primary source of income is not the norm. If a company would report that nowadays, it would trigger a money laundering investigation.
I'll bet they baselined 20% and started comparing it to the previous month or previous year. After many years, they probably established norms that accounted for this 20% loss unknowingly.
Probably not: their (1?) LRT line was just 1 chunk of their transit system, and systems generally have a weekly/monthly/student pass to uhhh, reward their heaviest users.