Go to every account (Skype, WhatsApp, Facebook, Google, etc) and uncheck the option to sync contacts. Go to Apps -> All -> And clear the cache and app data of all the Apps that sync contacts (Skype, WhatsApp, Facebook, Google, etc), and also of Contacts Storage.
Go to the Google Account and check the option to sync contacts. Let the phone finish the sync. All contacts shoudl now match the online Google Contacts.