Just now I went to Commons for the first time in a long time. I saw I had unseen notifications, so I opened the panels. In both cases, I as pretty sure I had seen the notifications. Now those notifications were "seen" on Commons, so I went to Hebrew wikipedia. Again, the same two notifications (one in Alerts, one in Notices) were shown as unseen, with the red and blue badges showing, the animation on panel open, etc.