I am by NO MEANS an authority on this (recently joined), but I believe it is a glitch that they are working on. I have the same problem.
Why does my profile continually say that I have 5 notifications? I check all my notifications, yet the 5 still remain. It never goes away!
I have the same problem. I found if I click notifications a second time while on my notifications it seems to clear it out.
There was a bug report concerning this matter. They are aware of it .
There has been an ongoing problem with that. I have a 126 notifications stuck on mine at present. One reason why I encourage people to use the Chat section or the Message section instead of making so many comments. We addressed it some at our Skype meeting but they still haven't been able to fix it and it's been months. I'll bring it up again soon and see if any progress has been made.