Original report: https://www.mediawiki.org/wiki/Topic:Szzz0c6h6bu7tgbo
We don't bundle revert notifications, so when this user asked someone on Commons to mass-revert 1000 of their edits, they got 1000 reverted notifications. Beyond the obvious issues related to spam (i.e. inability to find any real signal in the noise), this leads to an interesting issue.
Revert notifications are alerts, so they are marked as read when seen in the panel. Only those notifications that are seen in the panel will be marked as read (25 at a time), but the panel doesn't seem to realize this and sets the number of unread notifications to zero. So the badge starts out with 99+, changes to 0 when opened, then changes to 99+ again when you navigate to a different page (you do in fact have fewer unread notifs now, but a number in the 900s minus 25 is still greater than 99), etc etc.
It also appears that for this user, the notification panel got stuck in a loading state, but I'm still confirming that with the user.