This will happen if you click an alert, read to the bottom of that page of posts in the thread, and fail to notice that there's another page with new posts in that thread. If you then move on to another thread without first visiting that page with new posts, the status of the thread will remain "Unread" and so you won't receive any new alerts about it, since from the perspective of the forum software you've simply already been alerted and haven't caught up on the thread yet. You only receive alerts about threads that are not "unread".
I make this mistake fairly often. To get around it I make visiting the
Unread Watched Threads page part of my FC reading routine. For more info on that, check out my guide in the Community Discussion Lobby
over here.