There are different kinds of "pops" you might hear when stretching seriously. I will attempt to define what you might experience in a given stretch, and if what happened was good or bad for you.
1: You are stretching your groin, for example, and as you push your knees down, you hear a pop. It does not hurt, and all of a sudden. you get down further than before. Your muscles feel warm. What happened? You probably tore an adhesion between your muscles. Muscles should slide along each other. From a lack of stretching, or due to an old injury, you can have the connective tissue surrounding one muscle get adhered, or stuck, to another. If you stretch and tear this adhesion, you will be helping your stretch, and rid yourself of scar tissue between muscles.
2: You are practicing the sideleg stretches, for example, and you hear a pop behind the knee of the extended leg. Your extended leg is locked, there is a little pain, but not unbearable, you are not sure if you should continue. What happened? You probably tore a tendon, and you should probably stop and fold your leg into itself and let it rest for a few minutes. If it does not hurt after you get out of the position, it's probably ok. If it continues to hurt, stop and rest it. Tendons attach muscles to bone. You do not want to damage that connection. If there was a little bit of an adhesion and it let go, no problem. But if you did some damage, stop immediately. Rub out the muscle, maybe ice it. We would put a martial arts linament called teh tah chu on such injuries, which helps to heal muscles by bringing blood to the area.
3: You are practicing the splits. One of your legs is not quite straight as it should be. You hear a loud pop behind your knee, followed by pain. You probably tore a ligament. Ligaments attach bones to bones. Tearing a ligament is almost always due to improper stretching technique, or getting into a stretch too hard and fast. Ligaments have poor blood supply, and when they heal, they often heal with a lot of scar tissue (if you really tore it up badly). Stop your practice and rub out your knee. You might need to see a health care professional if it does not feel better in a few days (for these type of injuries, massage and acupuncture are most helpful).
These are just examples, but are common types of injuries that can occur when stretching. Go slow, and pay great attention to detail, and you will minimize, if not eliminate, any injury potential.