Let’s Encrypt sends an email for every certificate issued if the cert has not been renewed and this cert expires in 20 or less days, that means, if you for example issued a cert for domain.tld and then you issued a new one but now the cert covers for example domain.tld and www.domain.tld, Let’s Encrypt will check both certs and will send mail notifications for both certs.
Maybe you have issued several certs for your domain/subdomains but you are only using/renewing one, you won’t receive mail notifications for this one but you will for the others because you are not renewing them (mostly because you are not using them anymore).
If you provide your domain name we could take a look to know what is the actual case. If you want to check it yourself, visit https://crt.sh and search for the certs issued to your domain.