We are optimising a site which have sub-domains. The site structure is like this; main site is abc.com, sub domains are - tr.abc.com, ae.abc.com like that. The problem was when we started offpage 3 months back sub domain was ranking in the UAE region. Now after offpage link building, in June 2015 only main domain is ranking in Google SERPs. N.B. there is no hreflang implemented
My guess would be that you have too much duplicate content in your categories, tags, widgets. Check the density of your main keywords... try to lower it to 1% and try to optimize more for semantic keywords.