This can happen sometimes when you are using an email client like Microsoft Outlook or Outlook Express to check your messages. In the Advanced options of the email account there is an option called "leave a copy of message on server". Sometime configuration changes within your email client or computer can cause messages to be inadvertently re-downloaded.
To avoid this from happening in the future open your email clients Advanced settings. In the server messages area you can select one of the two options to delete these old messages:
- Remove from server after X days
- Remove from server when deleted from deleted items