I had that happen when somebody tagged me in a private repository that was later deleted (?).
You can fix it through the API by generating an API token in your settings with notifications permission on and using this (warning: it will mark all your notifications as read up to the last_read_at day):
Yes private repos that are deleted leave notifications behind.
GitHub has been experiencing mass waves of crypto scam bots opening repos and mass tagging tens of thousands of users on new issues. Using the issue content body to generate massive scam marketing like content bodies.
I got hit with one of these, then commented on GitHub meetsn issue about it, and ironically got a hundred notifications for everybody's comments, many complaining about phantom notifications.
Interesting that they went with a custom MIME type and a custom version header. I would have expected the version to be in the MIME type, but I feel like there is a reason behind this.
You can fix it through the API by generating an API token in your settings with notifications permission on and using this (warning: it will mark all your notifications as read up to the last_read_at day):