I am not 100% sure whether this is a bug or somehow intended by Bethesda. During Before the Storm when first arriving at Whiterun, the gate guard will stop the player. This guard often has a two-handed weapon assigned. I wonder if this guard accidentaly pulls the weapon from the leveled lists for Stormcloaks or Ulfric aligned guards. As far as I remember the other Whiterun guards carry imperial weapons.