You may not be leaning forward far enough when you have the bar on your back. If you have your arms out in front of you, or a plate or a dumbbell, that forward weight counteracts your too-upright torso and allows you to squat all the way down, no problem. Otherwise, you generally won't squat further down into a position your body realizes it won't be able to maintain balance in/get back up from. I remember not understanding this back in 2005 when I started working full time as a personal trainer, and wondering why I couldn't squat. Because the image I had in my head was a smith machine squat, which of course cannot be achieved by a free-standing human being. When I learned and realized that no, you need to lean over when you squat to maintain balance, suddenly I no longer had that problem.
Try learning over/sitting back more as you descend.
It's also not terribly uncommon for people to need a little weight on the bar to help shove them down in the proper position. I always feel my empty bar sets are worst, in terms of technique, and it gets better and easier to achieve good form as my warm-ups get heavier, and then as I get to working weight, I must once again really focus to keep good technique. I've observed this in many, many people who I coach as well.