The signature is generated using the key of the issuer certificate. Right now, the issuer certificate is R3, which has an RSA key. That's why you see an RSA signature on your ECDSA certificate.
One day soon, Let's Encrypt will have an ECDSA-only issuance hierarchy: Chain of Trust - Let's Encrypt - Free SSL/TLS Certificates. Once that happens, the issuer will be E1 rather than R3 and you will see an ECDSA signature.
Just to be clear: you have an ECDSA certificate, despite it having a sha256WithRSAEncryption signature. That's doesn't make it an RSA certificate.