I actually really appreciate a response like this which shows some level of human engagement. It would be better if they got these things right in the first place of course.
I worked for a TOC dealing with these sort of complaints (once they had been responded to by first line agents) and unfortunately poor knowledge of the overall systems was endemic. Unfortunately it is not considered a particularly skilled job despite the huge amount of knowledge that you realistically need on ticketing, routing, the law (I needed to reference the bylaws, RoRA, CRA, GDPR, PRO and the Equality Act at various points in some level of detail), rolling stock, payment systems, internal processes, external processes. We had a pretty comprehensive 6 week training programme but if you don't have any previous knowledge or interest in the railways, it barely scratches the surface.
Edit: there is also a culture issue I often encountered around the railway always being right. I certainly encountered a number of employees (including managers) who just could not accept the fact it was possible for the customer to be right about a member of staff doing a poor job, or that a ticket sold by Trainline created a contract and an obligation on the TOC, or even staff who insisted that any off peak ticket could only ever be valid after 9:30am - and that the printed restriction codes didn't mean anything. This culture of always being right compounded the issues caused by poor knowledge.
Unfortunately as with everything these days, it's far easier (or more profitable) to churn out keyword based copy and paste responses in the hope 90% of people will give up (and in my experience, they do) than pay people to do a decent job.
