Unlike many of the cosmetic changes to DU4, the underlying functionality of the sidebar notifications is brand new, so I'm not too surprised to see some quirks cropping up here and there.

You might want to try just dismissing these notifications and waiting to see what happens when new ones pop in... you can dismiss them by clicking on the little "X" at the top right of each notification, and they'll disappear.

After you do that, if new notifications keep coming in but they're still pointing to old threads, please let me know.