Usually this error means you specified the wrong webroot directory. Certbot should re-create the .well-known directory automatically if you delete it, though. Did you move the site to a different webroot after you originally created the certificates?
Check the configuration in /etc/letsencrypt/renewal and confirm that the webroot directory is what you expect it to be.
If you manually re-create the directories and create a file in .well-known/acme-challenge/test.txt can you access that file with a web browser?