ApplePay requires a private key to work properly. You need to save that key in a file and inform our plugin of the correct place of this key. For example:
- Correct: /var/www/htdocs/apple-pay-cert.pem
- Wrong: www.example.com/store/apple-pay-cert.pem
After that, flush the Magento 2 cache.
If the issue persists, try generating a new private key and following the steps on how to setup ApplePay in Magento 2.