Yes you got the option, but did you check it? Do you remember if you set the language of the 3 duplicate categories using this option?
I still haven't found the reason for this bug. Your answer may help me.
Waiting for this, I wrote a small plugin to correct the database when someone gets this issue.
*Make a backup of your database*
Copy paste in a file correct.php
Upload the file in the plugins directory
Activate the plugin -> it should immediately remove duplicate tags and categories
Deactivate the plugin and delete it