Once you have started working on mobility in your upper back, hips, and ankles from the past three weeks of posts, it is time to start re-training proper squat mechanics.
For a number of reasons, people forget how to move their bodies properly to squat. When asked to perform a squat, the knees shift forward and weight shifts to the balls of the feet as the heels come up. This places a lot of strain on the knees and overtime results in major knee issues.
A proper, safe squat is initiated at the hips. You should initiate by shifting your hips backward slightly (think a slight shift to shut a car door when your hands are full) and then start to lower your hips down by bending your knees and keeping the weight on the heels of your feet. At no point should the weight get onto your toes. As you go down, the knees should track in the direction your feet/toes are going.
If you have proper thoracic mobility, hip mobility, ankle mobility, and good trunk control, you should be able to get your hips/butt below your knees and be in that position comfortably, without any pinching or pain. Yes, your muscles are working so you may feel fatigue, but it should not be painful.
To stand back up, you push through your heels, think about screwing your feet into the floor to activate your gluteal muscles and keep your knees tracking outward, and stand up.