In Savage species several sample monster classes give feats at certain levels. Are these supposed to be feats in addition to feats they get via hit dice or do they count as the feats from the hit dice?
The feats listed in your monster class ARE the feats you get from your hit dice.
Specifically as per p.27 of Savage Species, your total feat count and other things like your skill caps all line up with what your hit dice get you on Table 2-5: Experience and Level-Dependent Benefits on p.15.
For convenience, at the levels when you get a hit die, the extra benefits from Table 2-5 are listed in the "special" column of your monster class, including new feats. This column can also contain certain feats that the monster would get as bonus feats.
As an additional note, the ability score increases from Table 2-5 are often staggered over monster levels such that their advancement doesn't line up exactly with hit die advancement, but all the monster classes I could find always lined up their feats with hit die advancement.