It’s not really whether they may be ‘magic spells’ or not though, as in the game everything is referred to as ‘Skills’.
Skills apply Physical damage, or Elemental damage (fire, water, earth, air, poison). Physical damages physical armour, and Elemental damages magical armour.
Skills may also additionally apply a status effect (knocked down, bleeding, burning, frozen, etc). Some status effects are blocked (‘resisted’) by physical armour, some are blocked by magical armour.
Just so happens that Geomancy (which is primarily an earth/poison Elemental damage school) has a couple of skills that apply some physically-resisted status effects like knocked down and crippled. It’s not a bug, nor is it stupid.