If I may offer a physical therapist's point of view...
First, no exercise is ever contraindicated for everyone or for every situation.
However, the reason knee extension exercises get a bad rap is related to closed chain mechanics (essentially the foot on the ground with some exceptions) and open chain mechanics (essentially the foot off the ground with some exceptions).
In a knee extension exercise on a leg extension machine (open chain) there is greater compression of the patella (knee cap) on the femur and also greater anterior tibial (tibia = shin bone)translation or shear at the knee joint due to a reduced recruitment of the knee flexors (hamstrings, gastroc, popliteus). If you have or have had any form of patello-femoral pain, chondromalacia patellae, anterior knee pain, or internal derangement of the knee (meniscus tear, ligament sprain or tear, chondral defect, etc.), the open chain knee extension is typically contraindicated as it commonly aggrevates the condition.
This is also quite common in cases of machine based hack squats and squats on a smith machine as the hamstring involvement is also reduced.
In the closed chain exercises which involve knee extension like a regular barbell squat, leg press (because of the greater hip extension moment the hamstrings are still strongly involved), lunge, step-up, etc. the patellar compression and tibial shear forces are much less as the hamstrings are co-contracting throughout the movement. That is why in rehabilitation situations, such as post surgery, therapists typically stick with closed chain exercises. They are deemed safer and more functional as the knee rarely functions in the open chain manner.
Also keep in mind that shear forces and patellar compression increase with the depth of the squat, so if you are symptomatic of some form of knee pain, deep squats may also be contraindicated. If you are asymptomatic, then ass-to-the-grass squatting should not be an issue if your flexiblity will allow proper technique and you follow some form of periodized training plan.
Hope that helps
Bill Hartman
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