I've noticed this a few times now with the new "sticky" inbox. I'll get two comment reply notifications close together, which will show a
2 badge over my inbox icon in the top bar.
When I open the inbox though, it will only show one reply. If I mark that reply as read, I need to close the overlay, then reopen it to see the other notification in order to mark it as read.
Now, I could probably just use the "Mark all as read" button to skip needing to open it a second time, but this seems like buggy behavior. I do not know what exactly causes it since I don't receive replies often enough to notice a pattern. It seems to be when I receive multiple replies from the same question though.