Crepitus in the knees may be caused by knee injuries such as meniscus tears. These are fairly common in people who play sports, jog, or run. A meniscus tear can cause crepitus as the joint moves. Chondromalacia patella is a dull ache behind the kneecap, usually caused by overuse or injury. There will be damage to the undersurface cartilage covering the kneecap.