The vast majority of guards / conductors / RPIs are sensible people and will accept the ticket as an issuing error as others have said, but the booking clerk should never put a traveller in the position of having to explain why they have a wrong ticket in the first place.
Once you pointed out the error the ticket should have been cancelled and re-issued with an apology and without question. At the very least the clerk should have endorsed 'Issuing error - Wrong R/C' and stamped the back of the ticket with the booking office stamp.
If it was not endorsed in this way and any Guard / Inspector had picked it up s/he should withdraw it and issue a 'zero excess' to allow you to complete your journey without further inconvenience
The reason behind this is very simple. The conditions applicable to the two railcards are different.
I know some people think 'it's a lot of hassle over nothing', but it isn't a good enough reason for not doing your job properly.
Any authorised RPI / guard etc could have withdrawn the ticket and put the traveller to inconvenience because of the unacceptable attitude of a booking clerk. Yes a Penalty Fare Notice could result because with no endorsement the traveller has no evidence that the 'clerk said it was OK'.
A PF is not a 'fine', though I understand why many people use the word. In monetary terms that's exactly what it is, but in law it's a 'civil remedy'. An opportunity to resolve a matter without more serious action being taken.
Yes, any PF should be quashed, but why should the traveller have to suffer the inconvenience of dealing with that just because the booking clerk was a lazy ******.
If it happens again, remind the clerk that if s/he refuses to correct their mistake you don't want to be awkward, but that you will submit the ticket with a formal complaint.