I have a new community, and one of my first users contacted me to report how she's getting duplicate notifications, two for the same reply.
I belive that is happening to her because when replying, it tags the person you are replying to (@username), which is great, but then you can get a notification for the criterion of being mentioned AND the criterion of being replied to, resulting in the person receiving two notifications for the same activity.
The notification for one or the other could be disabled, but that could result in no notification received in other circumstances so is not the right solution.