Unfortunately, I'm also experiencing Apple Pay issues. I posted a new thread about a week ago not realising this one was going, so here's what my issue was (and still is today) below;
I have an iPhone 6 128gb running iOS 9.0.1.
I had two Halifax bank cards successfully activated and had been using them via Apple Pay without any issues. After visiting the Apple Store last night to fix a camera issue, they decided to replace the phone instead. I successfully restored the replacement iPhone from an iCloud backup; I was able to activate one of the Halifax bank cards, but not the other. Here's a screenshot from trying to add the 'problem' card;
I also get the same result when trying to add to my Apple Watch. Again, both iPhone and Watch worked faultlessly before the replacement.
I contacted Halifax, they could see no issues at their end. They confirm that the cards are active on the iPad, and that the problem card is showing as having been deleted from the old device - even the time stamps they have tie in with the visit to the Apple Store. After checking my account, they say that I should be able to add the card and to refer to Apple for further assistance.
UPDATE TO ABOVE:
I'm now on iOS 9.0.2. Today I contacted Apple. They checked my iTunes account to confirm there was no 'debt' owing. They confirmed my bank card details were in order, and couldn't see anything obvious. They asked me to sign out of iCloud on my iPhone and then sign in again, which had no effect. The last resort was to reset the iPhone and setup as new, without restoring and to then add cards to Apple Pay. I did this and still have the same problem.
Now I've restored to my latest backup using iTunes. I've re-paired my Apple Watch, too. Neither device will accept the card. Just to confirm, this card was working perfectly, before.
Halifax confirm that they only have one record of said card which is linked to Apple Pay on my iPad. They tell me that the iPhone and Watch records show the card was deleted right before I received my replacement iPhone, so the problem has begun since leaving the Apple Store. I called Apple Store and the person I spoke with had never come across this issue before and referred me to Apple Tech Support - hence all the above steps.
Interestingly, I seem to recall trying to add the card in the Apple Store and got as far as requesting the security activation code to be sent by Halifax. I never had a phone or data signal in the Apple Store, and never received the activation code by text. I do wonder whether something's got 'stuck' somewhere without a trace. It may not be the reason for the issue, but worth mentioning.
If anyone can help me I'd really appreciate it.
Thanks in advance.