A court will throw the book at them and then beat them to death with it.
You can't take off "admin fees" for wages lol. If it also pushes them under minimum wage that is a separate offence.
It's possible that HMRC will get them before a court does. HMRC does check for that sort of thing and follows through. I suppose it's possible for a company to obfuscate or simply falsify their payroll and get away with it, but that would be very risky. Lying to HMRC is not something they let slide easily.
If HMRC finds out (and they probably will, sooner or later), they contact every affected employee directly and tell them how much HMRC thinks their employer owes them. They're extremely strict about it - if they think your employer has underpaid you £10 over the last 5 years, they will chase it up. And no, I am not exaggerating. They will give every affected employee a case number and tell them to get in touch to report what has happened (or not happened). The employer also gets informed, in detail, exactly how much they should pay to who and that they have a very limited time in which to do it. If they don't, HMRC initiates legal proceedings. If the company loses, they have to pay double.
Paying under the minimum wage as a result of charging employees a fee to correct an employer's payroll errors would not fly. They'd have a hard time finding a lawyer willing to offer that defence in court and make a laughing stock of themself. I agree with Nasher that a court would throw the book at them, but I think there would be a delay while the court wonders if that was really what was being offered as a defence.
Surely there must be a misunderstanding. If a company was breaking the law, printing it on wage slips would be a mind-boggling level of incompetence.