Differences in behavior between these two fly species is probably part of the story. Horn flies spend most of their time on the animal. They suck small amounts of blood frequently and leave only to lay their eggs on fresh cattle droppings. This constant presence on the animal means they are certain to come in contact with some of the insecticide and be killed.
Face flies spend only a small amount of time on the animal. Usually, they are off resting on vegetation. They visit the face, primarily under the eyes and around the mouth. Insecticide residues may not last as long on these surfaces, or the fly may not remain on the treated area long enough to pick up a lethal dose.
However, some of the newer synthetic pyrethroid insecticides are active against flies in such small quantities, that much better reduction in face flies is seen.
Source: Lee Townsend, Extension Entomologist, University of Kentucky College of Agriculture