The bug where the Deleted Comment appear in the notification inbox has recently started occurring for me.
This is what I see now:
The circled comments links to: https://gis.meta.stackexchange.com/posts/comments/3667?noredirect=1, But there is no such comment on the question, or any of the answers.
There is also this post which just gives the cause of the bug, but doesn't go into whether the bug is solved or not.