Hammering knee-dominant exercises with the goal of hypertrophy is kind of like playing Russian roulette. Sure, doing tons of compound work like squats, lunges, and leg presses and topping it off with isolated work like leg extensions will skyrocket your training volume and emphasize the target muscles.
But remember, the four synergistic muscles that make up the quadriceps group all insert onto the same structural point on the knee: the patella. And altering the kinematics, stability patterns, and general movement patterns of the patella in coordination with the rest of the body can be a recipe for some angry knees and maybe even injury.
The knee joint is quite simple. It's a hinge-type joint which moves into two degrees of motion: flexion and extension. While these biomechanical movement restrictions create more inherent stability at the knee, they also make it susceptible to chronic flare-ups, especially when volume is programmed haphazardly.
If your knees aren't happy, lighten up and try this.
Keep constant tension on the quads (don't stop or lock out at the top) and make the sets last at least 30 seconds. Your knees will be happier and you'll still build some big, strong legs.