Clicking on a notification (e.g. a user's reply to my comment) does not take me to the proper place in the comment section of a thread if the thread has multiple pages of comments.
I have to try each page and scan the entire thread for my avatar in order to find the exchange the notification was telling me about. It would be very nice if the notification link just jumped directly to the reply.
It might also be helpful if the comment you're directly linked to was highlighted in some way in the CSS. A slightly brighter background or border or something.
I used to have this issue, but I don't have it anymore. Notifications jump to where they should; the links point to specific comment IDs within a thread. Can you list steps to reproduce it? What do your notification links look like?