I'm not sure if this is strictly Discover related, but I have been using Apple Pay with my AMEX for a while with no issues. Just last weekend I added my new Discover card, I went to Macy's, it didn't work, went to McD was told that the machine was broken. My wife and I both thought it was a very weird coincidence, the fact that things stopped working/broken the day we added the Discover card.
But fortunately the next day, I had it working at several other stores that takes Apple Pay. Maybe it was just a bad day for Apple Pay/Discover? Why did you go through with the purchase though? We went to best buy and the moment they told me they are not taking Apple Pay my wife told them to void the transection and we just talked out.