You should examine the certificate presented for which the browser gives this error.
First, is it actually your certificate from Let's Encrypt? If the certificate doesn't say it was issued by Let's Encrypt, then it's some other certificate, for example a self-signed certificate provided with the server, presented due to a configuration error.
Second, does one of the names in the certificate exactly match the name of the server in the URL ? It is not good enough that they seem similar to a human, for example www.example.com and example.com are different.
If you are not sure how to check properly, I suggest running the https://www.ssllabs.com/ssltest/ SSL labs test on your site and reporting what that says if you still aren't sure what to do.