Users getting duplicate mails in their POP3 clients.
The issue was happening due to server Notes.ini parameter POP3_READ_ALL=1 .
Using the INI parameter POP3_READ_ALL=1 will let the POP3 client pop all messages regardless of their read or unread status.
You should be certain to NOT leave messages on the server when using this INI parameter, otherwise duplicates will be downloaded to the POP3 client.
Disable the option "leave mail on server" in pop3 client if you need to enable POP3_READ_ALL=1.
Do not configure multiple POP3 clients for same user because if the mail is downloaded by the first POP3 client it will be marked as READ and then it will not be downloaded by other POP3 clients.
You can use either IMAP or iNotes (Webmail) or Traveler as an alternate options to POP3 if user need to have multiple clients and devices to access mails.