The most common cause of popping joints is joint friction. when two pieces of bone in a joint, such as a ball and socket, rub against one another as you move. Sometimes it is also cartilage rubbing on bone. According to yoga instructor Paul Grilley, writing for Yoga Journal, joint friction is usually no cause for concern. You might not want to go out of your way to do it, but in the normal course of life it is harmless.
Snapping Hip Syndrome
Snapping hip syndrome involves a tendon called the iliotibial band, which runs from the buttocks to the knee. When the tendon becomes too tight against the bone in the hip, it can make a snapping or popping noise. This may occur because the band it too stressed or because tensed buttocks muscles are drawing the band tight. It may cause some inflammation and discomfort in the hip as well as the knee, but it is usually treatable through stretching, icing and/or massaging the band.
Risks
Most cases of a popping hip will not yield any risks. However, as with snapping hip syndrome, inflammation may develop in the joint, and there can be swelling if a tendon or bursa sac becomes aggravated or damaged. According to the Library of Congress' Everyday Mysteries, excessive popping may lead to some soft tissue damage, although the effects can be minor.
You shouldn't have to worry about any popping going on in the hip joint. If the noise can be eliminated by adjusting your sit-up position, consider making a change. Some hip popping may be unavoidable
Warnings
If you experience sharp pains when popping occurs in the hip, you may have a condition more serious than joint friction. Hip bursitis could be the cause, or a burst bursa sac. These conditions do not pose any significant threat, but they can be debilitating for a short time and force you out of certain activities to let the healing process occur.
I have this problem without Pilates. I've been told that there is only a small area for all the blood vessels, ligaments and tendons and muscles that are in the ball and socket joint. It's not a bone problem or you would know it. It's a soft tissue problem. And, yeah, it's very painful, especially when getting up from a seated position or anywhere low to the ground.
Even though you are doing all those stretches with Pilates, you should get in to physical therapy and maybe even a chiropractor. You need the correct exercise for the hips.