I haven't noticed that, but I don't think that's the problem. That is happening because my domains where being proxied by cloudflare. I disabled the DNS check on the settings and now it's not giving that warning again. Still, there is no sign of the hostname on the let's encrypt output:
[information] TasksCron: Searching for tasks to do
[information] Task4 started - Rebuilding froxlor_bind.conf
[information] Cleaning dns zone files from /etc/bind/domains/
[debug] domId domain ismainbutsubto parent domain list of child domain ids
[debug] 1 bruxiris.xyz 0 -
[debug] 4 diogomartino.com 0 -
[information] `/etc/bind/domains/bruxiris.xyz.zone` written
[debug] Generating dns config for bruxiris.xyz
[information] `/etc/bind/domains/diogomartino.com.zone` written
[debug] Generating dns config for diogomartino.com
[information] froxlor_bind.conf written
sh: 1: /etc/init.d/bind9: not found
[error] Error while running `/etc/init.d/bind9 reload`: exit code (127) - please check your system logs
[information] Task4 finished
[information] Running Let's Encrypt cronjob prior to regenerating webserver config files
[information] Checking for LetsEncrypt client upgrades before renewing certificates:
[Thu 22 Apr 2021 01:52:59 PM UTC] Already uptodate!
[Thu 22 Apr 2021 01:52:59 PM UTC] Upgrade success!
[Thu 22 Apr 2021 01:52:59 PM UTC] Installing cron job
3 0 * * * "/root/.acme.sh"/acme.sh --cron --home "/root/.acme.sh" > /dev/null
[information] Updated Let's Encrypt certificate for bruxiris.xyz
[information] Updated Let's Encrypt certificate for diogomartino.com
[information] Updated Let's Encrypt certificate for pma.diogomartino.com
[information] Updated Let's Encrypt certificate for roundcube.diogomartino.com
[information] Let's Encrypt certificates have been updated
[information] apache::createIpPort: creating ip/port settings for 185.11.167.250:80
[notice] 185.11.167.250:80 :: namevirtualhost-statement no longer needed for apache-2.4
[debug] 185.11.167.250:80 :: inserted vhostcontainer
[information] apache::createIpPort: creating ip/port settings for 185.11.167.250:443
[debug] 185.11.167.250:443 :: inserted vhostcontainer
[information] apache::createVirtualHosts: creating vhost container for domain 7, customer diogomartino
[information] apache::createVirtualHosts: creating vhost container for domain 9, customer diogomartino
[information] apache::createVirtualHosts: creating vhost container for domain 1, customer diogomartino
[information] apache::createVirtualHosts: creating vhost container for domain 4, customer diogomartino
[information] apache::writeConfigs: rebuilding /etc/apache2/sites-enabled/
[information] apache::writeConfigs: rebuilding /etc/apache2/htpasswd/
[information] apache::writeConfigs: rebuilding /etc/apache2/sites-enabled/
[information] Froxlor\Cron\Http\Apache::reload: reloading Froxlor\Cron\Http\Apache
[notice] Checking system's last guid