Yes, I realise that, but perhaps some more details.
This is, I know, somewhat historic but seemed to be a good example of the penalty system encouraging perverse behaviour. It concerned my experience travelling (weekly) from Wellingborough to London just after the morning peak. At that time MML routinely 'non-stopped' trains South of Leicester. On al bad but typical MML day, I set out to catch the 10.08. This was 'cancelled' but ran through non-stop about 10- 15' late. It was then announced that the 10.37 was 'cancelled' and that, similarly ran through without stopping. The 11.08 did stop; but, quite pointlessly because it carried 3 trains-worth of passengers from Market Harborough and Kettering and was impossible to board. I did manage to squeeze on to the 11.37, being prepared to stand in a doorway.
The non-stopped trains were only 10-15 minutes late and presumably this course of action was taken to avoid the difficulties you outline, although (unless turn - round times were far too optimistic) logically it was primarily to avoid the penalty. My original post made the point that the construction of the penalty system meant that an operating company avoided the penalty of late arrival by effectively cancelling trains with a resultant delay of 1 to 1 1/2 hours to all the passengers from Market Harborough, Kettering and Wellingborough (to be fair, more than an inconvenience, and to more than a few) without apparent trade-off penalty.
It's suggested above that there was a penalty for 'non-stopping' at the time (but possibly not for stopping a train with no space available) - which makes MMLs actions even more inexplicable - but it's unfortunate, in my opinion, that so much of the incentive/penalty system is not, apparently, readily available to the general public despite their interests both as prospective passengers and as tax-payers.
At that time, MML was offering extremely cheap tickets from Derby, Nottingham and Sheffield - the cheapest fare from those stations being about the same as the Wellingborough day return fare (with nothing cheaper) - and the service was 2 or 3 car 170s; I wondered at the time whether the real reason for non-stopping was simply that the trains were full & standing by Leicester (and the late running was caused by slow boarding), and that this was the real reason for not stopping. It rather sabotaged the attraction of the 'new, more frequent service' for passengers South of Leicester, though.