Hi @javinievas,
Take a look to this announcement Preferring IPv6 for challenge validation of dual-homed hosts
As a resume, your domain has 2 ips, one for ipv4 and one for ipv6. You have an apache on ipv4 and a nginx on ipv6. Let’s Encrypt is trying to validate your domain with ipv6 (nginx).
Cheers,
sahsanu