They did; the article even points out that there were two audits that showed the discrepancies: > The failure to catch him, despite discrepancies between fares

They did; the article even points out that there were two audits that showed the discrepancies: > The failure to catch him, despite discrepancies between fares and cash raised in two audits, was put down to a belief that the errors were software glitches and, after his arrest, led to a significant amount of internal finger-pointing.