One could fill up a composition book with the list of expenses a shop faces and in addition to what mark9207 listed there’s always that expensive issue of employee wages, benefits, uniforms, health care plan, etc, and of course the always present workers compensation premiums.
Speaking of markups, look at a hospital bill anymore. Many years ago one used to get a bill that stated the patient owed X dollars. Now it’s broken down into dozens of items and services.
Think about that 5 dollar band-aid, 10 dollar Tylenol tablet, or 15 bucks for a one-use pair of surgical gloves and consider the markup on things like that.