Deleted Mail duplicates itself

Whenever I delete an email, it duplicates itself as a unopened new email.
How do I stifle this annoyance, or is it some script/code written into the sender's email. Doesn't happen with all email, but nearly all, and especially if I signed up for alerts from somewhere (i.e. comments to video I have posted on YouTube).
Thanks in advance.

Verify/repair the startup disk (not just permissions), as described here:
The Repair functions of Disk Utility: what's it all about?
After having fixed all filesystem issues, if any, and making sure that there's enough space available on the startup disk (a few GB, plus the space needed to make a backup copy of the Mail folder), try this:
1. Quit Mail if it's running.
2. In the Finder, go to ~/Library/Mail/. Make a backup copy of this folder, just in case something goes wrong -- e.g. by dragging it to the Desktop while holding the Option (Alt) key down.
3. Locate Envelope Index and move it to the Trash. If you see an Envelope Index-journal file there, delete it as well.
4. Open Mail. It will tell you that your mail needs to be "imported". Click Continue and Mail will proceed to re-create Envelope Index -- Mail says it's "importing", but it just re-creates the index if the mailboxes are already in Mail 2.x format.
Note: For those not familiarized with the ~/ notation, it refers to the user's home folder, i.e. ~/Library is the Library folder within the user's home folder.

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