Cracking and popping noises can be attributed to a few different phenomena. One explanation is that when a joint is pushed into or out of its normal position (which could be done during a yoga pose) gases, primarily nitrogen, are displaced and escape from the synovial fluid inside the joint, causing a popping sound.
Another reason for the noise, according to frequent Yoga Journal contributor and international yoga teacher Judith Lasater, comes from a tendon moving across a joint or from arthritic changes that have already occurred in the joint. She believes that if this popping occurs naturally during yoga practice, or in daily life, for that matter, there is not a problem.
However, it is unadvisable to continually try to pop one's joints (i.e., cracking the knuckles). This practice tends to create hypermobility and can lead to instability in the joint. This instability can cause the surrounding musculature to tighten up a bit to support the joint and thus the urge to pop will arise again, says Lasater.
If the popping is from a tendon moving across a joint or from arthritis, continue to pay attention to the area, and if the symptoms change, or if there is pain associated with a popping or cracking noise, seek the counsel of a qualified health professional.