Are you familiar with how certificates and CAs work in general? You don't <i>receive</i> a certificate from the CA, they just sign and <i>attest</i> that the one you made is owned by you. The ways CAs go bad is not breaking any crypto but by signing a certificate that you don't own. This vulnerability is well known and LE takes industry-leading steps to mitigate it via the certificate transparency program which is a permanent auditable log of all certificates they sign.
As a centralized piece of software that has made itself responsible for safely massaging millions of private keys, certbot would certainly be a juicy target for NSA to compromise.
Betteridge's Law says "No" ... and given certificates are generated locally, I don't see how the certificates themselves could be compromised. The trust in a certificate (or trust in a false certificate) could potentially be manipulated in by and upstream party.
I suppose it would be trivial for them to issue compromised certificates or record the private key in a targetted attack for a specific domain without anyone noticing.