No, you wouldn't email. There are other automated options in that case. See: Revoking Certificates - Let's Encrypt
The most likely reason for the error you see is a damaged pem file. I don't know why you'd need to download it from crt.sh. If it was one of yours I'd think you'd have a copy already.
In any case, you said it is a public leaf cert so please either post it or give a crt.sh link (or similar) so we can try to reproduce the bug you see.
You should also explain how you installed Certbot and what o/s you are using. You said "nginx" was your o/s but that isn't an o/s.