Your ballcock is making the noise. As the water fills the toilet either the water pressure is to high or there is some object in the ballcock causing tubulance in the water. When you flush the upstairs toilet, remove the tank lid. Then as it fills up and the noise starts pull up on the float rod and stop the water coming into the tank. You will be able to find which ballcock is the problem one. Do the same to the downstairs toilet too.