A lot of people perform the squat barely going even 50% of the full range. Full range squats provide for better range of motion and activates the muscles to their optimal max. Full squats ensure that the glutes, hamstrings and quads are hit properly unlike in half range where a lot of tension also develops on the knee joints.
A lot of people do not have the mobility to perform full squats and hence propagate against it without knowing the real reason for the discomfort. In fact, full squats are an indicator of better muscular development and strength.
Full squats are a great realization of the real weights you can lift in full range. People squat heavy pounds with barely any range and end up injuring the spine with bad rep range and motion. Full squats require you to sit down completely and get up which ensures that you are mentally and physically prepared for the weight rather than pushing excessive heavy weights. Full squats also help ensure stronger and injury free knees as a 2013 analysis suggests that the highest compression force on the knees is at 90 degree angle.
So next time you enter the squat rack make sure to go as low as possible and if deep squats are getting difficult, maybe it’s time to get a check of your mobility as well as strength.