Are you suggesting that the notifications should be cleared/empty when you have read everything you’ve been notified about? Why would you want to do that? Is it because you don’t want to be distracted by them, or for some other reason?
Notifications are highlighted when you have not clicked on them yet or looked at what the notification is about. Then once you’ve handled them they are no longer highlighted but still listed. Personally I think this is great because it gives you ready access to recent discussions you have been involved in.