The notifications won't be marked as read unless you click them. Given that you have unread notifications, I think that the grouping behavior you describe makes sense.

Is there a problem with notifications not being marked as read despite you clicking them?

Or, do you think that we should be marking the notifications as read when you reply to the associated comment, or when you view the page?

@Whatamidoing-WMF: are you able to describe what the impact(s) the current behavior had on your experience? E.g. did you come to doubt whether you had in fact responded to comments that you thought you had?