Goldfish belong to the family of carp. Carp are a fish that feed on the bottom of their environment. In "the wild" this means rooting through mud bottom of a pond, or moving smaller stones and such along the edges of the pond, slow stream. IN the fall, the fish will feed on the steady rain of insects that fall on surfaces of the water, but most of the rest of the time, feeding is done almost exclusively on the bottom.
Our goldfish have this same instinct - which is why they feed most often on the bottom of the tank. They will eat the food that is easy to find as it sits on the top of the stones right after you feed them. But, after the "easy" stuff is gone, they still do what goldfish do - continue to look for food.
A goldfish will suck up mouthfuls of the substrate of a tank and move it aside, sifting through it looking for food. This is why a mud or sand bottom will always be a bit hazy and cloudy - for the fish will never let it alone. We use stone in our tanks to stop this haziness. But that does not stop the fish from sorting through the stones, too.
It is a very common problem for goldfish to pick up stones that fit into their mouths, but cannot, easily, come back out. A stone stuck in the mouth of a fish is a very bad thing. To avoid this, you can go to very small stones (messy and the fish can accidentally eat them) or to larger stones (river stones of at least 2 inches in diameter) to prevent the fish from getting them in their mouths.
Having the larger river stones does not mean that your fish will not continue to play tank hockey with them. IT is a natural instinct. It can be very noisy when done at night - so be grateful you have never seen or heard them do it!!!!
For a quieter tank - I have gone bare bottom!