Actually, knee pain depends on how you're built. Aside from random tendonitis in my left knee I never had problems when squatting to parallel or just a bit higher. When I switched to atg I started getting really bad knee pain within a few weeks and shortly after tore two chunks off my meniscus in my right knee. Not blaming deep squats entirely, but they were definitely a major contributing factor.
Op, you're a strong kid and those squats were plenty deep. Props.