I was having troubles with my web server, so I ran letsencrypt multiple times...after fixing web server issues (at least I think I fixed it), I now get a different kind of error:
[emerg] 25687#0: a duplicate default server for 0.0.0.0:443 in /etc/letsencrypt/le_tls_sni_01_cert_challenge.conf:15
This sounds like Nginx, right? FYI, Nginx isn’t yet fully supported, so expect to do some hacking at the source code to make it work. Also, if you are debugging, you should pass --server https://acme-staging.api.letsencrypt.org to use the staging server. That way you will avoid using up the issuance rate limits for your domain.
That said: Try looking in /var/lib/letsencrypt/IN_PROGRESS for generated intermediate files like that one.