Most fitness enthusiasts typically tend to overemphasize flexibility training, to the neglect of developing functional strength while in the stretched position.  Significantly improving your joints’ range of motion without also improving the strength of your surrounding musculature (especially at its new range of motion) can be an invitation for injury.

For example, when you improve your flexibility (in a given joint or group of joints) to the point where an additional five degrees of motion exists, the affected muscles now have a reduced amount of overlap between the actin and myosin filaments, resulting in a substantial reduction in force output ability.  For this reason, strength and flexibility training programs must occur concurrently.

During the stretch, the fibers elongate as each sarcomere extends to the point where no overlap between the thick and thin filaments exists at all (specialized elastic filaments comprised of titin keep the sarcomere together in the absence of overlap).  At this point, the remaining stress is taken up by the surrounding connective tissue (sarcoplasmic reticulum, sarcolemma and endomysium).  If the stretch tension escalates beyond this point, microscopic tears develop both in the connective tissues and within the sarcomere itself.  Such microtraumatic injuries eventually heal, but at the cost of scarification and micro-adhesions that may leave the muscle fiber less capable of contraction and extension.

Rather than short, intense bouts of stretching (which tend to trigger the proprioceptors), opt for longer, frequent periods of stretching where less tension is used.  Soreness after a stretching session is a sign that hydroxyproline (an amino acid found in connective tissue) and other biochemicals have been released into the muscle fiber to help repair damaged tissues.  It is probably a sign that you are stretching too hard. 

Warming up before stretching is important in two regards. First, core body temperature is elevated. Second, muscles are subject to thixotropy, which is the tendency of gels (e.g., body fluids) to become less viscous, following a period of being shaken or otherwise disturbed by outside forces. This explains why periods of inactivity tend to cause muscular stiffness, and why muscular viscosity is reduced when muscles are active. The most appropriate time to stretch a muscle (from the perspective of body temperature and the thixotropic effect) is after training.

International Sports Sciences Association (ISSA)  8th Edition Text

People often wonder why there are so many injuries in baseball when it is the least physical sport in terms of running, jumping, or physical contact.  Stretching is just another form of physical fitness and should not be taken lightly.  I have added a few thoughts worth considering when planning to stretch.

1. Be sure to improve strength while improving range of motion.  

2. Although you may use stretching as a warm-up, such a practice is often counterproductive. 

3. Prior to performing stretching exercises, core body temperature (not surface) must be elevated. 

4. Always stretch after intense workout sessions.