I find this case interesting.
In short, it seems he travelled Newton-Flowery-Piccadilly and intended to return Piccadilly-Flowery. For whatever reason, at the Manchester barrier he bought a return from Flowery-Piccadilly.
By buying a return from Flowery-Piccadilly, he made no attempt to pay for his travel on portion Newton-Flowery. Now, from the court's perspective, it needs to be established if he really did travel Newton-Flowery - in this case he admitted it, but if he hadn't lack of voucher/CCTV etc could be used to prove that he in fact did. Regardless, he admitted that he travelled from Newton, so lack of voucher is irrelevant.
If he hadn't admitted travelling Newton-Flowery, I'm sure the court would have ruled he had no obligation to keep any voucher given, but travel could still be established by witnesses or CCTV.
So, by not buying a ticket valid for travel on portion Newton-Flowery at the first opportunity, he committed an act constituting fraud (a misrepresentation of facts relied on by Northern Rail). To be guilty of fraud though, you need to also actually intend to do it. In this case, I suspect the courts found that this element did not exist - he obviously made a mistake.
However, this is pretty thin ground, as realistically it's an excuse anyone could use. The courts do have to be satisfied beyond reasonable doubt that one intended to commit fraud however.