If you're doing ATG squats and you're over, say, 5'10"ish (though there's skeletal variation), it's impossible to do a squat without the knees going over the toes (simply because of the proportions of your femur to your tibia). I'm pretty sure this myth started on idiotic bro-science forums like bodybuilding.com or the like.
On the contrary, there is absolutely no way this started on bodybuilding.com. Even a quick Google search attributes Karl Klein with this brilliant myth