These two statements are equivelent:
1) dont let your knees go in front of your toes
2) keep your weight on your heels
Try it. Its not possible to get your knees in front of your toes with your CG over your heels.
If your knees are going in front of your toes you are doing a "knee squat" which can easily mess up your knees. A proper squat has you moving your butt back to sit on that imaginary chair.
Dont think about knees and toes, its too hard to do and can distract you. I find its far simpler and better to focus on where your weight is because you can feel that with your eyes closed. If your weight is on the balls of your feet then you are in trouble. If your weight is on your toes, call 911 now. If the weight is on your heels, you are good.
My friend who studies fysiotherapy just got done with the whole legs, he got pretty damn good grades. He told me that knees going in front of toes can mess up your knees.
there's your problem. What people are taught tends to be wrong or different in practice. That's why personal trainers and academic people with no experience tend to know a lot of false things.