I noticed that when going through my notifications that when I click on one it doesn't immediately move it to the Read list, and when I open the notifications menu again the same item is still there.
Here's an example where I clicked on the first notification and it took me to the post, and you can see when I re-opened the notifications the notification is still there.
The problem with this is that when I'm going through all my notifications I get a bit confused about which item I'm up to. I realise what was happening was that I kept clicking the first item and kept getting taken to the same page. If I refresh the page it updates properly.