If a market participant is of the opinion that
their own authorised reseller is entering into contracts on their behalf which aren't lawful in some way, they must raise this themselves, up to and including legal action, as a matter of urgency, seeking to correct it at the earliest opportunity. Not to do so would strongly imply to me a tacit approval. To post something which contradicts the information applied at the point of sale at some other location, such as a Web page which there's not even a link to, doesn't seem terribly relevant to anything.
Of course, likelihood is that the real explanation here is that EMR aren't aware of the problem, or if they are aware of it, haven't taken steps to resolve it. Once the OP's contact is read they then would be aware, of course. Whose fault is this? I don't know rightly, but it plainly isn't the OP's.
I don't doubt those with legal expertise, but its not half daft in the 'court of common sense' that a third party retailer can make incorrect claims about someone else's service and then it's the service provider themselves who are on the hook.
The private company gets the money (via commission, ad revenue, selling data, whatever) but its the government-funded train operator (so indirectly the taxpayer) that's on the hook for costs dealing with the subsequent reimbursement or whatever when the service which they themselves never actually promised, wasn't delivered? As a third party retailer you could just claim whatever you wanted to in order to drive sales and leave the fallout to someone else. The law can sometimes be a very strange beast.
I would expect if EMR paid compensation to a consumer in these circumstances that they would have a very strong case indeed to bill that back to the retailer, no doubt with their reasonable costs of complaints handling and an administration fee added on. I don't think there's too much inconsistency in the law here. I think the problem is entirely one of the combined industry's own making.
Also consider what would happen if you couldn't rely on what authorised third parties said. You would always have to double check everything you saw on a retailer's website/app. You couldn't be certain the ticket you bought was valid for the trains you selected. Customers could be penalised for travelling with tickets they entirely legitimately thought were valid.
Even without the point about tickets being deemed invalid it would definitely be absurd to interpret the contract in that way. The Consumer Rights Act also offers a pretty easy statutory basis to read the contract as being in the consumer's favour here. Only one of the three parties is a consumer...
