No, you are not responsible for the hypospadias of your son.
To date, the exact causes of this disorder have not been found out: many factors are suspected. Today’s research focuses on molecular and genetic factors, the role of hormones, and even harmful environmental factors during sexual development of the fetus are being considered.
Whatever the cause, accept the hypospadias of your son as the result of several factors beyond your control. Do not seek the blame or responsibility of being a parent.