I few thoughts:
- Which challenge you want to use http or tls? obviously you cannot use both
- when it does not work
docker inspect
your container and look at thetls.domains
label. Does it look right to you? - Is your external dns for mysite.org and site.mysite.org point to the same traefik IP?
- Do you have something like CloudFlare (or other proxy between LE and your traefik instance) that might be filtering requests?
If nothing of the above helps try doing the same with let's Encrypt CLI from the same host to prove that this is not infrastructure problem and cert generation works without traefik and with LE.