I've had this happen too. The credit card selected in Apple Pay works when used directly in the Jewel payment machine, but not the Apple Pay instance of the same card. Also, Apple Cash gets the same error even though there is plenty of money on it.
What's most frustrating is not knowing who to call. Clearly its not the credit card company or a debit vs credit issue. According to this thread it sounds like a Jewel issue, but when I was in the store I asked for a number to call and they said there isn't anyone they can think of to call and he believed it was a card issue.
It doesn't seem like an Apple Pay issue either because it works fine at other stores.