When you try to create a website in CybperPanel, for example, for sub.domain.com, it ends up trying to request certificates for www.sub.domain.com as well as sub.domain.com, and generally, in this case, the www.sub.domain.com does not exist, which leads to the SSL certificate request failing.
It would be a good idea to give the user a choice to review and edit the sub-domains list CybperPanel is going to request SSL for through LetsEncrypt.
The odd part is even though the SSL request fails, CyberPanel reports that the SSL was successfully generated.
Here is another person stuck with the same problem.