This issue will only occur when downloading mail via POP3. It is not something to be seriously concerned about, we do recommend that you use IMAP however, which all major mail clients support. 

If storage on a mailserver is ever restored from backup, mail which has already been downloaded from the server may be contained within the backup, and will be re-downloaded. It is recommended that you contact support in these instances, but it is typically nothing to be concerned about.