Many of my patients develop TMJ symptoms as a result of orthodontic treatment, particularly treatments that involve extraction of teeth. Orthodontics as taught in most dental schools in this country, is primarily focused on tooth alignment, not jaw alignment (known as dental orthopedics).
Proper orthodontic treatment should involve diagnostic repositioning of the lower jaw prior to the start of tooth movement. Jaw alignment should be the foundation of all orthodontics. To move teeth without knowing if the jaw is aligned is like building a house without a foundation.
With abnormal alignment of the jaws a wide spectrum of medical conditions can arise (see Associated Medical Pathologies). I have a newly posted article explains a better way of treatment (Perils_of_orthodontics).