LetsEncrypt was vulnerable to this exact attack - it let people issue valid TLS certificates for domains they didn't control:
https://www.agwa.name/blog/post/duplicate_signature_key_sele...
https://www.agwa.name/blog/post/duplicate_signature_key_sele...
IIRC: it was missed by both an academic analysis of LE and a 3rd party audit of their crypto design. Thankfully Andrew spotted it a few weeks before they went live in major browsers!