Pain from habit, work, and life.

A knot in a muscle starts out as a micro-trauma or tear due to daily activities and stresses such as working, exercising, habit, hobby, over exertion, or just moving around, life.
Pain from pressure points that are deep within the muscle structure of the body can be caused by excessive habit, leaning to one side while driving long distance, sleeping in the same position every night.
The body repairs this by filling in and pulling the muscle together with scar tissue. This is on a micro-level and not very noticeable. Once it recognizes a spot to heal, the body will continue to treat that area as if it still needs repair. This causes more scar tissue to build up, causing more pain and less range of motion. Since the scar tissue is not aliened with the muscle, circulation in this area is slowed just enough to deposit cell wastes. An example of this is how dust collects over time, not immediately noticeable, but it adds up.
The body compensates for this automatically, sometimes the person doesn't even notice that they can no longer reach their arms up or even turn their head.