There was a situation where I replied to a thread and then someone replied to me and I didn't get an alert. Usually I get an alert in that situation. What reason could there be for me not getting an alert?
Unless it happens consistently, I wouldn't worry too much about it.
The only other thing related to watched threads is you will only get an alert for the first new post since you last viewed it. I'm not sure if there's a scenario that could have happened which would have been affected by that.
Aside from that, you may be looking at an issue with an add-on, but hopefully it's just a one off.
Then you're definitely talking about something completely unrelated.
Regardless, the likely cause for that is that an add-on has created an alert for a user, but the alert is then filtered out when the user opens their alert list.
It can also happen if the alert has expired. Alerts expire after 30 days by default. For performance reasons, the alert count isn't totally dynamic. It's a cached value. So if a user receives 5 alerts and doesn't visit for over 30 days, the alert count will read 5, but in fact they are all expired.
This isn't necessarily true. If you get an alert and don't read the thread, the alert will potentially be removed but the thread will still be unread (and you won't get another alert). Vice versa, if you read the thread immediately, the alert will still exist but the unread thread won't be listed.