Let’s say I have manually requested a wild card certificate from Let’s Encrypt, and that’s certificate is still active, say *.example.com.
Now I have a Traefik web server that will automatically request a certificate for a subdomain of the domain above (say subdomain.example.com) but Traefik would not do this.
So my question is that will Let’s Encrypt refuse to issue a certificate for a subdomain that already covered in a wild card certificate also issued by Let’s Encrypt?
no, there is no automatic refuse. If a certificate is created, the job is done. So you can create a certificate *.example.com and later one with blog.example.com or other subdomains.
But: There are limits:
So if you have a lot of subdomain-certificates created (50 per week) or if you create 5 certificates with exact the same name ( blog.example.com ) in one week: Then you may hit a limit.