Have you configure delete inactive sep client offline ?
In version 12.1 of the SEPM, the location for adjusting the setting to delete clients which have not connected for X number of days has moved:
1.In the SEPM, go to the Admin page.
2.Select Domains.
3.Under Tasks, select Edit Domain Properties.
4.In the Edit Domain Properties window, on the default General tab, note the option to "Delete clients that have not connected for specified time.
Check this artical
https://www-secure.symantec.com /connect/articles/duplicate- sep-clients-appear-symantec- endpoint-protection-manager- console