My character takes damage whenever he hits Clannfears or Atronachs even though he's not being hit by the aforementioned enemies, what could be wrong?

It's perfectly normal. They have a Reflect Damage magic effect, which does exactly that. You can get around it by using spells instead. Not sure about ranged attacks.

DO'H! *hangs head in shame* They sure deal a lot of damage, my character has been killed many a time for that reason alone since I turned up the game's difficulty.