Read that notice again carefully ... you CAN amend to add the spouse (in fact you should NOT have filed single on the original return instead it should have been MFS on a mailed in return) HOWEVER you cannot get any of the tax credits on the kids OR the RRC (stimulus payment) when the spouse had an ITIN issued after the original due date of that return. So did they deny the joint filing or the extra credits ? The TT program may have given you credits you were not allowed because the interview doesn't take late ITIN applications into consideration.
