first of all I moved out a pending ssl queue by
mv /var/cpanel/autossl_queue_
then tried to issue the SSL and showing the warnings/errors which mostly causes due to rewrite rules in .htaccess
so I have renamed .htaccess and then able to issue the SSL, please check and confirm for the same.
After issuing the ssl I have moved back your .htaccess_bk to original .htaccess