The thing I find most interesting is the final snippet of the article:

404 Media found that MTA’s trip history feature still works even when the user pays with Apple Pay. Apple told 404 Media it does not store or have access to the used card numbers, and does not provide these to merchants, including transit systems. Apple did not respond when asked to clarify how the MTA website feature works when a rider uses Apple Pay.

Per https://www.apple.com/apple-pay/ marketing, "When you make a purchase, Apple Pay uses a device-specific number and unique transaction code. So your card number is never stored on your device or on Apple servers. And when you pay, your card numbers are never shared by Apple with merchants. Your purchases stay private."

So something strange is going on for sure...