That is a good point, unfortunately I only had one card that I could try it with.
I'd bet money that it's something with how the card is doing contactless on Apple Pay versus the real card. From what I've learned, there's two methods: magstripe emulation and EMV contactless. Some cards can do both in Apple Pay, while some can't (and same with the physical cards themselves). I've heard of this being a problem with US-issued Amex cards with trains in London - the card works, but Apple Pay doesn't.