There might be several reasons for this, poor technique and insufficient time for adaptation are probably the most common ones. Though previous injury is certainly another possibility. In general, squats are good for your knees, and will protect your knees from injury. Not only will they strengthen the structures of and around the knees, they will also (literally) lubricate the joints.
It takes time to develop a good squat. Many people seem to be limited by their range of motion, especially in the ankles, at least to start off with.
It takes time to develop a good squat. Many people seem to be limited by their range of motion, especially in the ankles, at least to start off with.