Every time a new post pops up in the right top corner, it shows it as a reply even though it is not.
At the bottom of each topic, you should see the following buttons:
If you click on the bell, you should be able to set the notifications you want to have. I guess that what you think is a reply is simply a new message in a thread you’ve already participated in.
You can also set global tracking settings in your user preferences: Preferences > Tracking.
No, it has the reply picture instead of the bell, which it should have.
I’m not talking about the bottom settings
Could you add pictures, then? I’m not sure I get what you’re talking about.
I suppose you’re talking about the notifications in the avatar menu.
All posts are replies except the first post of a topic. The notification doesn’t mean it’s a reply to one of your posts, just that it’s either a reply to one of your posts or a reply to a topic you’re tracking or watching.
Am I getting this right?
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A screenshot or a better explanation of the issue would have been helpful, as bugs exist 
There’s a known bug of duplicate notifications for certain badges, for example.