In addition to what Karin has already said, I assume you’ve observed his squat for any weakness in form. Did it start after you began training? What area of his knee? Did he use too much weight in his squats too soon? Is he overweight? You can see there are just too questions for us to give an answer on this one. 🙂 Could be anything, but if it persists I would also have him see a doctor.
Have him track when he feels his pain, and then refer.
beyond recommending to the person to see a physician, everything is speculation.
One possible cause could be an old injury, maybe even unknown the the person which had damaged the cartilage in the knee. Bits of that can get in the way with certain activities, thus causing the pain. But, as said, this is pure speculation. He should see a doctor.