If you have duplicate contacts across different sources then you'll need to enable 'Merge across sources' under Settings (gear icon at the right-hand side top corner) and then re-analyze. Also, select appropriate options under Settings-->Analysis Level and re-try.
Important Note: Merge across sources will merge duplicate contacts into 1 and will remove the duplicate from either of the sources.
If you have contacts with the only name as common, the app won't recognize such contacts as duplicates. It works on a combination of Name+Email or Name+Phone.