In one particularly notable example, a passenger was prosecuted for using a "+ via London" ticket and the Guard incorrectly believed that meant not valid via Reading. See:
https://www.railforums.co.uk/threads/taken-to-court-facing-criminal-charges-advice-needed.156920/
I got in touch with the passenger, I arranged for a solicitor (who is a member of this forum) who was going to win the case and then pursue XC for damages I had agreement from a company director to be an expert witness if necessary, I had BBC and other journalists on standby to report the case.. however the passenger did not trust me (as is their right) to get a good outcome, they paid a FOUR FIGURE sum to a solicitor who arranged for the case to be settled out of court (it went to an initial court hearing but no further), XC were not pursued for damages & costs, the customer was left thousands of pounds out of pocket and they wanted no media attention. All my effort was wasted and XC got away with it! The customer could afford to be a few grand out of pocket and just wanted to get on with their life. Fair enough, their choice, but it left me rather disillusioned to say the least. I even had the support of someone at XC though I can't really talk about that on here (I'll tell you next time you see me if you remind me!)
There are other cases where XC have been in a lot of trouble and had to pay compensation but I am not allowed to talk about them
(at least not yet... hopefully one day)
None of the cases I am aware of are due to "malfunctioning booking engines", though any tickets bought with an itinerary are contractually valid.