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A few of my clients reported receiving multiple/duplicate copies of the same email message at different times.
--- For example ---
They received an email message at 01:30 pm, an hour later they received the same email message again.
This does not happen with every email account on the server, but it does happen from time to time.
I am running the latest release of the WHM/cPanel. I re-installed Exim and reset mail inboxes and databases, but without much success. I have also made sure that there are no accidental duplicate forwarding or POP accounts.
--- Suggestions and possible solution ---
It is likely that the client's email program got disconnected before downloading email messages, successfully, from the server. That said, the server won't delete the email message or messages unless instructed to do so by the client's email program. It might be your client's have an unstable connection from either their ISP or from the server.
Another issues may be arising from the option "Leave mail on server" in the email program.
Please, check the Message-id header record of the duplicate email messages. If they are the same, then it is most likely a POP3 issue. If they're different, then there's something wrong at one or the other end of the SMTP email transfer.
One final thought, check the contents of the actual POP3 inbox file to see if they are holding duplicates. If not, then it is almost definitely an email client/connection issue.