Good job thinking it through! In fact, bones are often bruised when the ligaments that attach to them get torn. These "bruises" can't be seen on an X-ray. They can be seen with MRI scans. A bone bruise is like a small fracture of the bone. Most bruises will go away completely. But it's still unclear what the bone injury will mean in the long term.
Scientists are concerned that the initial bone injury eventually causes the bone to become less resilient--less "bouncy." With the shock absorbers down, the cartilage that covers the knee joint ends up taking more force. This can take a toll on the joint surfaces, and may lead to arthritic changes in the knee joint.