There are evidences that an excessive level of flexibility can result in a decreased degree of joint stability. There is a trade-off between flexibility and stability. This decrease in joint stability is particularly evident when the flexibility increase is the result of lengthening the connective tissue structures that stabilize a particular joint.
For example, Deep knee bends, may increase the range of motion of the knee joint to the point where the knee becomes more susceptible to chronic or acute instability.
As such, an individual's range of motion for each joint should be determined by the demands of the individual.
It should be noted that an excessive range of motion for a given joint could result in decreased stability and a greater potential for injury.
I have noticed a few trainers trying to stretch the clients joints by forcefully stretching even after knowing that they are too flexible. This kind of forceful stretching for an already flexible person does not aid, rather it will make your joints more susceptible to injury.
Strength training is the best way to deal with this problem. By doing strength training your ligaments (tissue that connects bone to bone) will become stronger and increase stability and thereby making the joint less susceptible to injury.
Remember flexibility is necessary but that does not mean you should try to touch you head to your feet.