Certbot gets 404 Not Found when trying to verify

[RobertoMC]

Please fill out the fields below so we can help you better.

I ran this command (domain.com and username were replaced):
/root/certbot-auto certonly --webroot -w /home/username/public_html -d www.domain.com -d domain.com

It produced this output:
The client lacks sufficient authorization :: Invalid response from http://www.domain.com/.well-known/acme-challenge/5W1ceYO_tlwxt4QNcGasdf234324

There is no .htaccess file

My operating system is (include version):
CentOS release 6.8 (Final)

My web server is (include version):
Server version: Apache/2.2.31 (Unix)

My hosting provider, if applicable, is:
NA

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):
NA

A test file in acme-challenge works OK:

curl -i domain.com/.well-known/acme-challenge/testfile

HTTP/1.1 200 OK
Date: Sun, 22 Jan 2017 17:08:55 GMT
Server: Apache
Last-Modified: Sun, 22 Jan 2017 17:08:19 GMT
Accept-Ranges: bytes
Content-Length: 20
Connection: close
Content-Type: text/plain

This is a test file

[Osiris]

The error probably had more text than you’re showing us now, correct? I.e., 404, 403 or something like that.

[RobertoMC]

Here is the whole thing:
/root/.local/share/letsencrypt/lib/python2.6/site-packages/cryptography/init.py:26: DeprecationWarning: Python 2.6 is no longer supported by the Python core team, please upgrade your Python. A future version of cryptography will drop support for Python 2.6
DeprecationWarning
Saving debug log to /var/log/letsencrypt/letsencrypt.log
Obtaining a new certificate
Performing the following challenges:
http-01 challenge for www.mydomain.com
http-01 challenge for mydomain.com
Using the webroot path /home/username/public_html for all unmatched domains.
Waiting for verification…
Cleaning up challenges
Unable to clean up challenge directory /home/username/public_html/.well-known/acme-challenge
Failed authorization procedure. www.mydomain.com (http-01): urn:acme:error:unauthorized :: The client lacks sufficient authorization :: Invalid response from http://www.mydomain.com/.well-known/acme-challenge/79El54TRfx5O1hLQBp8w7SYJIx3wTL-I_2ADNXcGM: "

404 Not Found

Not Found

<p", mydomain.com (http-01): urn:acme:error:unauthorized :: The client lacks sufficient authorization :: Invalid response from http://mydomain.com/.well-known/acme-challenge/oNsANFJAoqlPt3BEDorT_ft9OZYf7jlXU: " 404 Not Found

Not Found

<p"

IMPORTANT NOTES:

• The following errors were reported by the server:

  Domain: www.mydomain.com
  Type: unauthorized
  Detail: Invalid response from
  http://www.mydomain.com/.well-known/acme-challenge/79El54TRfx5Bp8w7SYJIx3wTL-DNXcGM:
  "

  404 Not Found

  Not Found

  <p"

  Domain: mydomain.com
  Type: unauthorized
  Detail: Invalid response from
  http://mydomain.com/.well-known/acme-challenge/oNsANFJAoqlPt3BEDorT_8v3Yf7jlXU:
  "

  404 Not Found

  Not Found

  <p"

  To fix these errors, please make sure that your domain name was
  entered correctly and the DNS A record(s) for that domain
  contain(s) the right IP address.