These are two exercises I like for this purpose:
Toddler Squat: https://www.youtube.com/watch?v=dc3V3f45nOI
I have people hold that position for 30-60 seconds, for either three sets, or have them spread it out during the day.
Harder version: https://www.youtube.com/watch?v=nQdPjpP5k8A
It's good to have something nearby to hold on to. Often the person will feel like they're going to fall backwards.
Another exercise: https://www.youtube.com/watch?v=DSSGeymXUgw
You can think of the latter as a horizontal squatting motion. Because resisting gravity and stability isn't a concern, it's easier. It's also a good assessment because of how relaxed the body can be. If after a couple weeks of working on this the person isn't getting anywhere, that's a good sign something structural is going on.
For instance, notice how this guy's lower back rounds when he rocks back:
However, notice once he opens his knees, he now has more range of motion before his lower back rounds:
Image source: b-reddy.org
This is due to how his hips are built. This gets rather anatomically technical, but you can see more details in the following links:
While the above is a discussion on hip flexibility -because that's what I've seen to be the most common limitation- the ability of the ankles to plantarflex (toes point down) has to be considered as well.
Knee wise, the range of motion is usually there. Unless the person has awfully tight quads, or has an injury history where they never regained their flexion range of motion. Not common issues.
Finally, not being able to get all the way is no big deal. Much like not everyone can do a split, not everyone can squat the same either. You want to be careful about forcing range of motion though. You end up jamming bones together, which can cause issues over the longterm. If you feel some tightness while stretching, that's a sign improvement can be made. If you feel a blocking, like you just can't move further, that's likely bone in the way. Pushing that will only make the matter worse. (Bone gets bigger when it gets pushed or banged on sufficiently.)