Beats me. Sometimes the re-notifications are because someone has added a new reply on that thread. Other times I think it's just some glitch in the program that doesn't quite know how to sort. Maybe it's designed to err on the side of repetitive to keep punters coming back. You know - how to train a pigeon to keep pecking a lever by sometimes spilling a seed.
It happens to me all the time if I use the list I get when I click on the bell. I have better luck when I select 'see all notifications' and then chaeck 'Mark all as read'.