So exactly what is the path where customers are seeing the confusing information?
When I use Apple Pay and want to see a recent transaction on my American Express card I follow this path,
iPhone > Wallet app > tap AmEx card > Latest Transactions > tap merchant name > transaction information.
I see the information below.

The merchant name and location is clearly displayed at the top of the screen and location.
You’re saying that your customers are seeing something similar? Can you please post what you and your customers are seeing? If you need to, just do a 1¢ transaction and void it later. I understand what you’re saying, but it’d be helpful to see it and it’ll confirm the issue.
Apple Wallet app does use GPS and WiFi to obtain a location. Apple Pay can only display the information the bank shares with it. Apple receives anonymous information that’s encrypted. Your bank provides most details. I suspect location information is first obtained from GPS. However, GPS signals indoors are weak at best and the system falls back to WiFi. If you locations/businesses don’t have a strong WiFi signal, the Wallet app uses information from nearby sources. Unfortunately, if a VPN is in use, the location could be misidentified.
You can verify this with a screenshot of a transaction.