This is not an error. This is because of a security feature from Apple Pay to protect your customer’s credit card number. When a customer pays with Apple Pay, it assigns a unique payment token which is saved in their system instead of the customer’s credit card number.
This payment token is also used by Clover, which is why the last 4 digits on receipts and the Clover device do not match the last 4 digits of the customer’s credit card.
Reference Site: https://help.clover.com/faq/when-a-customer-pays-with-apple-pay-why-dont-the-last-4-digits-match/