My son has several spots that itch, specifically his belly button, it is red & hard, a spot on his chest & the ridge around his penis.

Itchy Skin Rash: Your son has "several spots that itch" and is not scabies per your doctor. Itching is associated with a number of skin conditions and can be caused by allergic or inflammatory mechanisms. Eliminating scabies as a cause is a good start however making the correct diagnosis of skin lesions can be difficult. Continue to work with your doctor as a step-wise approach to diagnosis can take time.