Yes, it looks like either the Apple Pay servers cannot access your certificate or it was not able to be used for Apple Pay on the Web due to the Cipher Suites on the certificate.
1) Make sure the domain you are verifying is not behind a proxy.
2) That your certificate is using at least TLS 1.2 with one of these Cipher Suites (Prefer Elliptic Curve):
TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256
TLS_ECDHE_RSA_WITH_AES_128_CBC_SHA256
TLS_ECDHE_RSA_WITH_AES_128_CBC_SHA
TLS_DHE_RSA_WITH_AES_128_GCM_SHA256
TLS_DHE_RSA_WITH_AES_128_CBC_SHA256
TLS_RSA_WITH_AES_128_GCM_SHA256
TLS_RSA_WITH_AES_128_CBC_SHA256
3) If your domain is not publicly accessible you may need to provide access to these IPs for verification:
17.32.139.128/27
17.32.139.160/27
17.140.126.0/27
17.140.126.32/27
17.179.144.128/27
17.179.144.160/27
17.179.144.192/27
17.179.144.224/27
17.253.0.0/16
4) If you are unable to find the issue try setting the server access logs to verbose and retrying the domain verification. The logs should tell you where the breakdown is.
Setting Up Your Server
https://developer.apple.com/documentation/apple_pay_on_the_web/setting_up_your_server
Matt Eaton
DTS Engineering, CoreOS
meaton3 at apple.com