The whole system sucks. When I ran a limited company I had myself on the payroll and had to file a timely return every month through their software. Trying to find out just what I was supposed to do was a headache in itself.
Firstly I got a letter saying I'd missed a reporting deadline, so I called the number and asked what it was they were expecting me to report. When they explained it was a monthly PAYE return I said there was nothing to report because I hadn't paid myself anything that month, and asked if they could send me what I needed to register so I could file reports. They replied a month later with another letter saying I'd missed a reporting deadline. That time they were really kind, having not paid myself the previous month they assumed I'd paid myself that month and they also assumed exactly how much I'd paid myself based on, as it turned out, nothing more than a random number. When I called them they asked if I was calling to make a payment so I asked again just what it was they wanted me to do because I was desperately trying to comply with the rules. Guess what I got a month later....
I must admit when I wound up the company one of the things I was really glad to be rid of was the need to endlessly use their crappy software to explicitly tell them every month that there was no activity to report.
It's just par for the course, if there's a mistake then it's the individual's fault, whoever actually made the mistake. And if you accept in the utmost good faith that HMRC systems have calculated the correct code and tax due and they get it badly wrong, somehow it's still your fault.