If you have duplicate contacts across different sources then you'll need to enable 'Merge across sources' under Settings-->Advanced Settings and then re-analyze. Also, select appropriate options under Settings-->Analysis Level and re-try.
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 only name as common, the app won't recognize such contacts as duplicates. It works on a combination of Name+Email or Name+Phone.