I just wondered why there were 4 new notifications in my top bar, but none showed up in the list. In the list was just old stuff from yesterday. I had no possibility to say Alle Mitteilungen als gelesen markieren. I managed to get the number 4 disappear by marking one read topic as unread, and after that I could use mark all read, but still I had no clue what I had marked read, as even on Special:Notifications nothing was shown.
After that I went to my watch list, and there I saw 4 deleted spam posts for the Flow forum. I think they were the culprits for the ghost notifications. How come, that they are not markable without some minor hacking skills? Either they are in my notifications, or they are not. If nothing's in there, the number should be 0.