I get this problem as well... So here is a sketchy fix... Sometimes it works, sometimes you need to re do it. When I get a notification, of course I click it, and see the new notification. I then "go-to" the new item by clicking it. Once I've read or responded, I click the back button. Then I pull the screen down, thus reloading the notifications, (I'm on an iPhone) then I select "done" when I'm finished. Usually this process seems to work for me. If it doesn't work. Go back to notification page, reload the page by pulling down on it again, then click done when your finished...