Discomfort to the calf is minimal. The approved injection site for all growth implants is in the middle third of the back of the ear between skin and cartilage. Implants should never be placed in the muscle at the base of the ear because they migrate, affecting absorption of active ingredients and acting as a foreign body in usable muscle months later. Implanting pellets anywhere else but in the ear, or crushing them through faulty technique will also disrupt absorption patterns and give unpredictable results. Cleanliness is another important consideration.
Implantation is a surgical procedure.
Infection and abscessation means implants are wasted. I think the primary reason is that it's just one more thing to do. Producing beef is not getting easier. Gone are the days when spring processing meant blackleg vaccine and brands. Just getting a calf to market often overshadows getting the best calf to market.