Why do extremities in unnatural positions freak me out? is this an irrational fear?

Yes, but: It is an irrational fear, but you are not alone, given that this imagery is often used to frighten people in horror movies. It ties back to evolutionary issues ("caveman mind") and the way in which we are conditioned to draw toward those with an "ideal" form and to be fearful or avoidant of abnormalities in form due to concern for possible illness or disease.