im using the lastest ispconfig 3.1.12, i added a new site as Subdomains (Vhost) but instead of the ispconfig template welcome loading, it is loading a part of the main domain, i went to tools > resync but this did not fix the issue.
Most likely you have chosen a directory for the vhost subdomain which is inside the web directory of the main domain, so accessing the vhost subdomain must load a part of the main domain then.