The issue itself is not caused by ispconfig, but there are some genarl considerations that you should do for all hosted websites when it comes to duplicate content:
1) Create only the nescessary dns records. E.g. ceate a a-record for the domain and a a-record for the www subdomain and dont use wildcard (*) DNS records.
2) Dont use wildcard subdomains in apache. Check your website settings and ensure that you use e.g. auto subdomain www and not auto subdomain *.