Nearly always this is because you got several different certificates (such as possibly on for yourdomain.com and then realised you didn’t have the www version, so generated a new certificate with both yourdomain.com and the www version (or maybe mail. or something )
If you don’t think that was the case, what’s the domain name in the email ?
certbot takes the renewal information from the configuration, yes.
The email isn’t from certbot though. The email is from the Let’s Encrypt server which only knows about certificates issued ( not that you now want to use the new expanded one, rather than the old one). Hence it sends warning emails about the old ones. Once that has expired, you won’t get more emails about it.