Your muscles heal faster than joint tissues. Tendons, ligaments, and cartilage are whiter and receive less blood flow, so they are more sensitive to irregularities in nutrition and anabolic hormones. Your body can't keep up with your current program, diet, or lifestyle. I was developing chronic joint issues before I stopped eating polyunsaturated fats, but now everything is limber and pain-free. I was concerned I had permanently worn down my hip joint, but nearly everything heals if given the right circumstance. The key—I think—is to speed up every aspect of metabolism—not just muscle recovery—in order to keep joints healthy and resilient, and the thyroid is one of the main regulators of whole body metabolism.
Niacinamide cures a little bit of everything. Shining red light or sunlight directly on the knees may accelerate recovery by a lot. Light weight used to create a pump can bring instant relief (until the pump goes away). It could just be an acute injury—not chronic—but this is how the chronic issues start.