First, you need to login to the webmail to check whether there is any duplication. If the duplication only happens in the mail client, it might be because the internet connection is not stable or the size of the mail is too huge.
When mail client downloads mails on behalf of the user, the whole process in general would be as below.
1. Connection establishment between mail client and mail server through POP3
2. Upon successful establishment, signals (greetings and response) would be initiated and upon completion list of mails to be downloaded would be retrieved and the actual mail download would be executed
3. Upon download completion, all mails downloaded would be 'marked' and would then be removed from the server
With reference to the idea above, should there be any fluctuation on the the connection, whereby the mail downloading had been interrupted, the whole process would be started all over again from the first when the connection resumed. In this case those downloaded mails would be downloaded again since there is no 'mark' on them indicating that they had been downloaded previously.
If the user does not leave a copy of message in the server, the mail will be deleted upon download. So, the user can choose to leave a copy of the mail in the mail server in order to monitor on the situation.