Oh dear! Trust you don't now get prosecuted by a different department in a few weeks' time!
What could they be prosecuted for (with a reasonable chance of conviction)?
A Byelaw prosecution wouldn't be valid, as the ticket would have been valid at the time of travel.
Regulation of Railways Act s5(1) prosecution again falls at the first hurdle, as the ticket would have been valid if any staff member wished to see it.
RoRA s5(3) I don't think fits as it specifically mentions "previously paid his fare" (which is true, even if later refunded), along with the intent requirement.
I think this would normally come under a Fraud Act prosecution, but by reaching out to them and explaining the mistake - I cannot see how the requirement for a misrepresentiation to be made dishonestly could possibly be proven?
Criminal law generally allows for honest mistakes (strict liability offences such as found in Railway Byelaws are the exception, not the rule) - and even if we were to take an extreme (and probably unwarranted) view that they intended to defraud the railway but got cold feet - proving such is likely to be impossible, especially to the required standard of proof.