I think we have been over this before you have a rail card which you know you are not entitled to have and get discounts which you also know you are not entitled to receive. You are skating on thin ice - look what happened to this couple who found a cash machine which was giving them out money and not debiting their account:-
http://www.guardian.co.uk/uk/2009/apr/21/cash-machine-theft-essexThey now both have a criminal record. You could say they were just using a loophole.
Perhaps, but what FA is doing isn't as clear cut as the cash machine situation. As soon as the staff are in on the scam and tacitly condoning it ("I didn't think you are allowed this, but computer says yes so I'll sell you one") the legal and moral situation becomes alot muddier. Much more like realising the bank was giving you free money and telling them this only to be told by bank staff "don't worry about it".
In the days when I had a YP railcard and Bath Spa had a Travel Centre selling large format tickets, one of the machines in the Bath Travel Centre would apply the RC discount differently to the others and the discounted fare to London which I used to buy twice a week would come out 5p too cheap (or the tickets from the other machines were 5p too expensive - I never found out which). One member of staff in particular would sometimes get up from her seat and walk to "cheaper" machine that wasn't being used to do my ticket. I never asked for this but she did it a least a handful of times. Always with a comment like "every little helps" or "stupid computers". Should I have made a fuss and demanded to see her manager?