This issue also affects your ActiveSync mobile devices, such as the iPhone.
If you open one of these duplicate contacts, you will notice that the Notes field says the contact was added by Lync 2013.
This a caused by a bug in the Lync client, which adds a duplicate contact item every time you have do an IM with this contact. The bug will be fixed in the next cumulative update (CU) for the Lync 2013 client. In the meantime, here's how you can fix it.
The duplicate contacts are stored in a contacts folder called Lync Contacts. This folder is protected by Outlook so you can't delete it from there. You need to delete it from Outlook Web App, which does not treat it as protected.
- Log into OWA and view your contacts.
- Right-click the Lync Contacts folder and select Delete.
- Click Yes to confirm you want to delete the selected folder and move all contents into the Deleted Items folder. You can then sign out of OWA.
- From the Outlook client you'll need to empty your Deleted Items folder to finish getting rid of all the duplicate contacts. You'll then be free of them!