Read Aadil Palkhivala's response:
Muscles shaking after a strong practice can have a number of causes. First, you must understand that it is not desirable. Indeed, it is a symptom. One of two things has happened: Either you have overworked the muscle to such an extent that it does know how to go back to its original position, and therefore trembles; or you are irritating your nervous system by practicing too intensely or incorrectly, and a nerve is firing, causing the muscles to shake.
A strong asana practice, especially during youth, is highly recommended and has many benefits, but never should be violent. When the muscles shake uncontrollably, it is a strong indicator that the practice has been far too violent. Indeed, I remember my young, egoistic days, when after doing a strong practice with B.K.S. Iyengar, my muscles would shake for two or three days! This agitates the nervous system and prevents the sthiram (stillness and stability) and sukham (pleasantness and happiness) that Patanjali describes as being the desired effects of asana.
Having said that, there are times when a muscle has been so tightly contracted for so many years that, when it is finally released in an asana practice, it shakes uncontrollably because it does not know whether to be longer or shorter. This, however, is a temporary phenomenon.
The shaking could also be due to an awakening of a chakra or a subtle body realignment—this shaking does not happen often, though it is often strong. However, your question indicates that the muscle shaking is both frequent and intense. Thus, my guess is that you are overworking.
Recognized as one of the world's top yoga teachers, Aadil Palkhivala began studying yoga at the age of seven with B.K.S. Iyengar and was introduced to Sri Aurobindo's yoga three years later. He received the Advanced Yoga Teacher's Certificate at the age of 22 and is the founder-director of internationally-renowned Yoga Centers in Bellevue, Washington. Aadil is also a federally certified naturopath, a certified <a href="/health/ayurveda">Ayurvedic health science practitioner, a clinical hypnotherapist, a certified shiatsu and Swedish bodywork therapist, a lawyer, and an internationally sponsored public speaker on the mind-body-energy connection.