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This problem usually happens if you are trying to issue a certificate for a domain or subdomain that is not pointed to your VPS Ip address where webmin is installed.
So either point all domains and subdomains that you are trying to secure, or set specific domains in the box (in the SSL page)
Also trying installing Certbot manually by running the following command:
apt-get install certbot
Then try issuing the certificate again from the interface.