Double charging issue with Apple Pay linked cards

Somewhere, you other card being charged is set up for your a subscription. That is the only wya a second charge can be happening on a card you don't have added on your account.

1. Check out Apple ID for added payment methods. click here ➜ If you need to change or update your Apple Account payment method - Apple Support
2. Check accounts on the websites of the services you are using.
3. If you are subscribed to a service through Apple and through their website, you are subscribed twice so would get charged twice. Pick the subscription you want to keep and cancel the other one.

Apple Pay can’t initiate a charge/payment. Transactions are initiated by the merchant. When the merchant presents the charge, a payment is processed by your bank. If a charge is presented to Apple, the payment method on file is used to complete the transaction.

It sounds like you have either two subscriptions and you’re paying one directly and the other through Apple. Have you verified your subscriptions?

You can review your subscriptions through Apple several ways depending on the device you’re using.

You have signed up for a subscription in the Amazon app and on the Amazon website using a differently payment method. Apple has no idea if you already have a Prime membership when using an in-app purchase, but Amazon does if you are using the same account details. You can either cancel the subscription managed by Apple or the one that is managed by Amazon. I would also recommend following up with Amazon to make sure each subscription is showing the same account details and if so, request a refund from the one that is billing your payment method directly from their website.