Itching is not unusual after hair transplant and is often caused by dryness of the scalp. At three months, this should be subsiding, so follow up with your surgeon to express your concerns.
Though after 3 months the new grafts should not be effected by scratching, you should consult your physician about shampoo or topical medications to help diminish the itching on your scalp. Long term inflammation or irritation can damage the scalp and may lead to hair loss. Be sure to follow up with your transplant surgeon and see what they may recommend. Good luck