Comment visit tracking doesn't account for comment deletions
The comment visit tracking keeps track of what time the user last visited the thread, and how many comments there were at the time. One issue with this is that if any of the comments are deleted, all the visit-tracking on that thread effectively gets "behind" by one comment.
For example, say I visit a thread and there are 3 comments at the time. One of these comments is then deleted after my visit, taking it down to 2 comments. If someone else posts a new comment after this, the thread won't be marked for me with "(1 new)", because from the tracking system's perspective, the thread still has the same number of comments. It won't be marked until there are 4, and at that point it will still say "1 new" when it's really "2 new".
This is a bit of an issue that could be tricky to solve. When someone deletes a comment, it may need to decrement the comment counter on all visits that were stored between the time the comment was posted and the time it was deleted. This could be a bit heavy when there are a lot of users, so I'm not sure if it's a good idea (but I'm not sure there are other good options either).