I have noticed lately that I have replies to posts and comments, but no notification.
I noticed this post has 8 comments but I have no notifications, upon looking 1 is a top level comment and the rest are replies to that.
I have checked using Mlem, Blorp, and old.slrpnk none show a notification for that comment.
There have been others over the past week or so, this is just the first I investigated.