What makes the kitchen faucet knock when the water filter is in use?

Assuming you are talking about a RO/DI unit because this is in the saltwater aquariums categories, It happens a lot with pipes. The RO/DI unit does not have steady flow, therefore the pressure is constantly either decreasing or increasing. When that happens the pipes will shake. The knock you hear is the pipe hitting against something either under the kitchen or in the cabinet.