It sounds like your instance is hitting the timeout before getting a "message received" report from the recipient's email server. This is apparently more common with Microsoft Exchange, but it can happen with any mail server. If your mail server is having other problems you may want to wait until that's fixed before doing anything, because fixing the mail server will most likely fix this problem.
Instructions for fixing this are here: https://confluence.atlassian.com/confkb/email-notifications-from-confluence-are-duplicated-using-microsoft-exchange-server-660966544.html
For the sake of interest, here is a similar article for when it's happening in JIRA with a bit more information and links to some useful comments: https://confluence.atlassian.com/jirakb/duplicated-issue-creation-comments-or-notifications-280068481.html
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