The body it set up to alternate between mobile joints like our hips and ankles and stable joints like our knees and pelvis/low back. When one joint is too mobile or not functioning "normal," it has an effect on all of the other joints, especially those above and below. There is a common misconception that if you are flexible you should not have pain. It is important to think of the roles of the joint and how they interact with each other. If the joint and surrounding muscles have flexibility without stability and mobility, then it is not functioning properly . When unnatural forces are placed on joints it commonly causes dysfunction, degenerative changes, injury and pain.
By definition, mobility is "the ability to be moved and move freely and easily." In terms of joint mobility it is the degree in which a joint articulation can move without resistance or restriction of the surrounding muscles, tendons and ligaments. A person with good mobility is able to execute coordinated movement without resistance or restriction. This sounds a lot like flexibility, but the two are different.
Flexibility is the absolute range of motion and distance a joint and the crossing musculature can move. This motion can be uncoordinated, and adding excessive forces on the surrounding joints due to the lack of mobility and controlled motion. You can be flexible, but if you are unable to perform the motions with good balance, coordination, stability and strength then you could be setting yourself up for injury and pain due to dysfunction.
Stability is defined as the ability to maintain control of a movement by coordinating actions of the neuromuscular system. Stability is directly related to the size and shape of a joint and the surrounding ligaments. When there is damage to a muscle, the stability of the joint may still be intact anatomically due to the ligaments. Ligaments are designed to maintain stability within a joint and not allow it to move past its normal range of motion. That is why your knee is not nearly as mobile as your ankle or hip. A person with excessive flexibility is placing extra stress on the ligaments which can in turn cause a lack of stability and mobility.
Maintaining flexibility is important, but alone will not prevent or heal injuries. A combination of flexibility, mobility and stability within surrounding joints are needed to create controlled movements and prevent pain and injury. There are many mobility exercises, muscle activation exercises and stretches that are beneficial and help the body to function at its optimal level.