There are two main causes of running injury: structural imbalance and training volume. Both can lead to injury, and many times the cause of the injury is not easy to diagnose. For example a foot problem can cause a problem in the knees, hips, or back. Finding, and treating, the cause of a running injury is the job of a trained expert.
Structural imbalance occurs when the body is misaligned, or when a certain muscle group is weak and requires other muscle groups to compensate. Structural imbalances can be caused by physical attributes like uneven leg length or severe overpronation of the foot. These physical problems will cause running injury unless diagnosed and treated.
The body adapts to stresses and becomes stronger. This is the basic principle of training. But, if you push too fast or run too far, you can stress the body in such a way that it never has time to fully recover and weakens instead. Training progression and temperance are the keys to avoiding overuse injury.