As you probably know, the shared sites are set up as sub folders within the main site. You need to make sure that Google sees these sub folders only through their respective domain names, and does not see them as sub folders within the main domain. Otherwise, Google will think the pages are duplicates. You can control this in your robots.txt file of the main domain (i.e. instruct Google not to look at those sub folders when crawling the main site).
Best,
Christopher