Could he have used the ticket machine(s) instead? If these were working and accepted the method of payment your son intended to use, then in principle this was a valid circumstance in which to issue a Penalty Fare.
That being said, there are a few things to bear in mind. Firstly, many Penalty Fares are liable to be appealed on the basis that the warning signage doesn't comply with the requirements under the Penalty Fares Regulations. Signage must be prominently placed at every entrance to a station and must have certain required wording. Obviously, most people won't read it but it if it isn't there, Penalty Fares can't be charged. So that would be one potential ground of appeal you could use - it's worth noting that it's down to the operator that issued the Penalty Fare (either Northern or TPE, I'm guessing?) to disprove any allegation you make, not the other way around.
Furthermore, as your son is only 16, Northern/TPE would have difficulty pursuing a Penalty Fare in the civil courts. Once you bring a first-stage appeal (there are three stages of appeal) and that appeal is decided, they are no longer allowed to prosecute in the criminal courts in relation to that particular incident. Therefore, whilst I would not necessarily recommend it, you do have to consider what options they have if you simply don't pay.
Obviously you may just decide that paying £55 is the easiest option in the circumstances. It's also worth noting that tickets can be bought online or on many different apps and are available as e-tickets that can be shown on any digital device or printed off. So unless your son intended to use cash or another method of payment that's only accepted at a ticket office, he could likely have bought his ticket that way. There's no compulsion to use such methods instead of facilities available at the station, but if the train is about to leave and there's a queue at the ticket machine(s), it's one option that's available.