Yeah but we all know it goes on. Maybe not in this particular instance, however -'ve certainly encountered the odd iffy time, or alternatively the system being played to the limits of the rules so someone gets a green scorecard.
Wherever there's humans in the process there's at least the potential for pressure to be applied to get those all-important green squares on the scorecard.
(And, yes, I could provide very specific examples, but it's not appropriate to do so on this forum!)
The system is not bright enough to be able to distinguish trains well in some circumstances, but there are plenty of stakeholders involved to ensure that any incorrect recording is weeded out, due to the sums of money involved.
There may be one or two every now and then that slips through the net, but I doubt any such big discrepancy as the one the OP claimed would go unnoticed, as it will have an impact on performance figures which all TOCs will be keen to get right. I am interested to hear how these figures can be fiddled with if brought to the attention of someone as verification is not that difficult, and if a train is a minute late, it is a minute late. A train that is 20 minutes late is not going to be recorded as RT once someone has checked it.
Claiming that some staff deliberately fiddle with the statistics is quite an insult to everyone who works in performance management. The DfT takes such practice very seriously so no TOC will be foolish enough to do that.