Subway no longer supports Apple Pay. I tried to go there and use it and couldnt. I didnt have any cash on me so... they were out of luck that day.
I believe they still accept it, but the level of awareness in individual stores is low and I have encountered some who don't know how to make it work. Their machines also have some weird QRCode pay system which allows you to pay with their app. If the cashier hits that button for your payment instead of just hitting the button saying you are paying with a credit card, then the machine won't recognize an NFC payment.