I have had this happen several times: I watch a thread, but don't get any alerts when it has been replied to. Only by going through the "New Posts" do I later discover that there were actually new posts there since the last time I had seen it.
I know. I'm talking about not receiving an alert even for the first unread post. Sometimes I get it, and sometimes I don't.
Like currently, there's a thread on xenforo.com, watched by me. I have checked and read through it, and now there are no new unread posts in it for me. I and go do something else. I come back to xenforo.com, and see no alerts. I check New Posts and find out that the thread actually has had someone post in it.
To do any debugging, it's important that you don't view the thread when the problem occurs. When you view the thread, you destroy the data that we would need to check to debug it (the last read date in the thread).
If you can find the last alert/email related to a thread when you trigger the issue, that would help (though I can probably track it down in the DB too).