This is a very old argument, one that goes back almost twenty years. One way to look at this is to find out what the averages are for random donor areas where you can look at the percentages of singles and doubles. Some clinics will tell you that the percentage of singles in the donor area at any given time is roughly 15%, others will say maybe 12% while still others may claim 20%. This is assuming the patient is Caucasian as ethnicity does impact the percentages. Then look at how many singles they are getting for patients, if those patients are given and publicize their graft counts when they share their results. If the percentages vastly outweigh the supposed averages, then something is off. But, is this a bad thing?
The true artists in the field do not simply take and place grafts as they occur naturally. It is a common misconception that microscopes are used for "sorting" grafts (if microscopes are even used to begin with, and in most cases they are not). This is not sole purpose that their use was intended. No, experienced clinics (and their techs) know how to create the grafts that they need. If a patient has a particular need of singles that the donor supply isn't providing naturally, then the clinic will make them. For instance, if the patient needs a lot of singles for the temple points as well as the hairline, then this is the approach to be taken if there aren't enough singles to get the job done. It is the opposite approach that some clinics use for adding density where they will make a graft bigger than a single follicular unit by creating a graft with two follicular units. This is seen in FUT surgeries since you have a larger piece of tissue to work with and you don't want a punch used on your donor big enough to take to multi-hair follicular units. The way to do this with FUE is to "double up" two grafts into one incision.
Cutting grafts down into singles and, conversely, adding two grafts to the same incision can and does occur in the same surgery at some clinics, and there is nothing wrong with either. I think it makes more sense to NOT charge by the hair because it discounts the work that goes into creating the grafts. You have to be skilled to be able to pull off these approaches successfully, much less consistently, and while paying per hair may seem more fair to the patient, it isn't really covering the finer aspects of hair transplant surgery that separate one clinic from the other. This isn't to say that clinics that charge by the hair are bad, quite the contrary, but I think the argument that clinics that charge per graft just to make more money at the expense of the patient is a lazy point to make to patients that don't know any better.