When I've had replacement season tickets, the person has always just typed the photo card ID number in. Once they got this wrong (two digits transposed) and it was fun having to go through the process all over. Another time they printed it upside down (the whole railcard, not the number), but that's another story.
However, if you'd ordered the season online or perhaps gone to a different station, I always thought that when doing a replacement it would make more sense to use the details on file. In which case there might be the chance of the photocard ID being incorrectly entered, or mixed up with another one. I wonder how it's processed in the back office? A clever database system or a huge Excel spreadsheet or something silly!
If the OP is telling the truth, I'd hope that it can easily be sorted out and therefore agree with the comments about not bothering to talk about suing and compensation just yet.