What is the exact description of the charge you see on the card?
Your card could be compromised by using the physical card at a gas station or retail terminal that has a Skimmer device installed. The card number can also be given to a website where Apple has no control. Simply adding the card to your Wallet does not make Apple responsible for any charge made to it. You will still see those charges in your Wallet even though they did not originate from your phone. The bank that issued the card will be able to tell you the source of the charges. Disputes on the card are handled the same way whether it has been added to your Wallet or not, by disputing the charge with the bank. For charges that occur with an in-app purchase that Apple does process, you will see the Apple.com/bill on the charge and it can be disputed with Apple directly. For these charges you can request a refund here:
Request a refund for apps or content that you bought from Apple - Apple Support