2000 Ford Taurus brown coolant

I got brown coolant in the tank recently. Today I detached the tank and found there are some rust-like stuff in the bottom of the tank (some but not much). Then I installed the tank back and fill new coolant. But after I turned on the engine, the brown stuff just came back from the two above small pipes (or maybe just one of them. ) The heating system still works fine. I do hear some low noise (not sure how to describe, like rattling) when engine runs nearly below 2 rpm. Others look fine.