We released a hotfix today to address an issue that was causing multiples of the same email to appear in users mailbox sync folders for particular emails. While there was only one copy of the email in Soup Mail, it was sometimes appearing multiple times in the users sync folder in their mailbox. This was impacting some users who are syncing to Exchange 2003 servers over IMAP, because it was occasionally reporting malformed message-IDs.
The hotfix has resolved this issue, however, you will need to manually delete the duplicate from your mailbox if you have been impacted. Otherwise you can happily ignore the duplicates and sync will clean them up after they pass your recency window defined in your Soup Mail sync settings.