I can only account for this happening with my sniper, since I only use this class to target from long distances, but in 1 mission, the performance dropped significantly when I went into Free Aim. It was VERY slow trying to move to a body part. No other member of my party had issues with Free Aim, and I can only reference that their targets were closer.
The only scenario I can provide in this instance is my sniper was on the 3rd floor of a structure, and the visible target was on the other side of the map, ground level.