Can't see whats wrong here

[bdamage]

Please fill out the fields below so we can help you better. Note: you must provide your domain name to get help. Domain names for issued certificates are all made public in Certificate Transparency logs (e.g. crt.sh | example.com), so withholding your domain name here does not increase secrecy, but only makes it harder for us to provide help.

My domain is:
skipper.xen.prgmr.com
I ran this command:
Request LE cert from Virtualmin panel
It produced this output:
Saving debug log to /var/log/letsencrypt/letsencrypt.log
Plugins selected: Authenticator webroot, Installer None
Obtaining a new certificate
Performing the following challenges:
http-01 challenge for skipper.xen.prgmr.com
Using the webroot path /home/skipper.xen.prgmr.com/public_html for all unmatched domains.
Waiting for verification...
Challenge failed for domain skipper.xen.prgmr.com
http-01 challenge for skipper.xen.prgmr.com
Cleaning up challenges
Some challenges have failed.
IMPORTANT NOTES:

• The following errors were reported by the server:

  Domain: skipper.xen.prgmr.com
  Type: unauthorized
  Detail: Invalid response from
  http://skipper.xen.prgmr.com/.well-known/acme-challenge/PTu1r93r-67F1sZtmL5QxoJe2WklHxR_lfVKA68cx5Y
  [2605:2700:0:2:a800:ff:feca:9922]: "\n\n404 Not
  Found\n\n

  Not Found

  \n<p"

  To fix these errors, please make sure that your domain name was
  entered correctly and the DNS A/AAAA record(s) for that domain
  contain(s) the right IP address.
  My web server is (include version):
  Apache 2.4.41
  The operating system my web server runs on is (include version):
  Ubuntu 20.04.2 LTS
  My hosting provider, if applicable, is:
  prgmr.com
  I can login to a root shell on my machine (yes or no, or I don't know):
  yes
  I'm using a control panel to manage my site (no, or provide the name and version of the control panel):
  virtualmin 6.16
  The version of my client is (e.g. output of certbot --version or certbot-auto --version if you're using Certbot):

[rg305]

Hi @bdamage, and welcome to the LE community forum

Are you aware that name resolves to three IPs?

Name:      skipper.xen.prgmr.com
Addresses: 2605:2700:0:2:a800:ff:feca:9922
           71.19.148.107
           71.19.148.103

LE prefers IPv6 when present, so, as shown above, it will try IPv6 first (and will not fail-over to IPv4 when a response is provided by IPv6).
In this case, the response was negative and the authentication test failed.

Please ensure that your site works via IPv6 before continuing.

[Osiris]

I agree with @rg305: your IPv6 address returns an "Apache Ubuntu Default Page" while your IPv4 address(es) respond with a small page saying "There's nothing here.".

[bdamage]

Thanks very much. I just added the IP6 address and re requested. It all worked.