No, neither IN or Bonehead reduce your perks.
If you chose the Skilled trait, then you get 6 perks total, 1 perk every 4 levels. But otherwise, and normally, chars get 8 perks total this season, 1 perk every 3 levels.
So...it sounds like somehow you missed a perk. Please check your Perks list and tell us what perks you do have.