The exact same thing used to happen to me. I focused more on pushing with my glutes and quads and now they just get sore like the every thing else. Try checking out Chris Duffin's squat warmup. That seemed to help me a lot.
Also when I stopped reading Rippetoe's squat mechanics it helped me. I still low bar but now I try to keep my chest more upright instead of leaned forward, push with both my quads and hips instead of just hip drive, and push my hips through like a deadlift rather than straight up.