Hmm... OK it's just that the NPC building guide in the Core Rulebook doesn't mention the use of the favored class bonus in the building of the NPC listed there, but I guess in HL, you're actually building a character from the ground up instead of how they describe to build an NPC in the Core Rulebook.
I see one difference from the NPCs that Paizo builds to HL. The characters with class levels are getting the full HP for the class at level one when the creatures in the Bestiary are not getting the full hit points for a core/base class. I believe this is elsewhere as well, I did a random sampling in the GMG and it was like this. Example: Hobgoblin Fighter has 12 hp, while same stats and everything in HL will have 17 hp.