Usually it's that. If a thread has new posts you haven't seen, and more posts in it deleted than new posts since you last viewed it, then you get that message. (The watcher asks the server how many posts are in a thread, and what the timestamp of the last post in the thread was. The watcher remembers the number of posts and the last post's timestamp whenever you view a thread. If it ever gets a higher timestamp from the server than it remembers seeing itself, then it alerts you that a thread has new posts and it displays the number of posts the server says is in the thread minus the number of posts that it last saw in the thread, if that number is positive. If that number is 0 or negative, such as because of deleted posts, then that causes the "Unknown new" posts message. You can easily trigger this by watching a #cyclic tagged thread.)
Though I don't exactly understand what would cause it to get that error in a thread with no replies. That's an actual bug and I'm getting that issue too constantly when I watch the thread. I'll look into it now.