That happens to me too with some threads I'm following. I think it has something to do with not interacting with the thread when you receive a notification, like if you don't go in and comment or otherwise engage with the new posts it decides you must not really want to be notified.
IDK, that's the closest to an explanation I've come up with but I'm sure there is a valid technical reason which eludes me. Probably something about niggers and/or AIDS.
If there are multiple posts since you last checked it will only send you one notification, so in those instances you will not have the exact number of notifications as there are posts made in the thread. Could that be it?