Age factor may be associated with the pain that your father is complaining of in his joints.
Intake of lemon which is a very good source of vitamin C should not cause any pain. Although heralded as a powerful antioxidant that fights everything from the common cold to cancer, recent studies show that over a long period of time high doses of vitamin C are associated with worsening of one of the most common forms of arthritis - osteoarthritis of the knee.
Osteoarthritis causes the progressive breakdown of joint cartilage - a cushioning tissue layer that helps bone move against each other without causing friction and destruction of bone. But you have clearly mentioned that your father is not suffering from any other ailment. For confirmation however you can ask your father to eat a diet devoid of lemons for 3-4 days and see if the pain subsides or not. The other thing of concern in his diet should be the intake of salt. If he is taking lot of pickles, excess of salt is also going with them and that might be a probable cause for the pain he is complaining. Even otherwise salt intake should be only moderate in one's diet. One to two lemons a day should be just right for your father.