when my cistern fills up intermittently is make a loud noise as if some thing is vibrating as the water fills the cistern. Nothing appears to be loose in the cistern.
It will probably be the washer in the valve thats vibrating a bit...you can fit new ones but if you can't live with it a replacement is best. I use 'Torbeck' ones - quiet fill, side or bottom entry, really small and easy to fit.