D&D 3.5- For example a bugbear's humanoid levels give it two feats, does this stack with the first level feat or is the first level feat included? (all together 2 or 3 feats)
The humanoid type does not grant any special or extra feats
The statement that the bugbear has two feats from its racial hit dice is a reference to the fact that RHD are included as part of your level and therefore as part of your progress towards getting the usual feat at 1st and then at every third level. They just don’t want you to forget that the RHD count towards that.
So yes, the two feats they’re referring to are the ones you get at 1st and 3rd level. They are not two additional feats on top of those.
Note that the bonus feat granted by the human race is a feature of that race, not of the humanoid type.