Steel nails that are in contact with moisture will rust. Depending on conditions, this rust can either be red or black. Nail heads exposed to air will always be red rust-colored. If the nail is extracted and the nail shank is red, then the wood is saturated with moisture. Damp wood that possesses a high amount of tannic acid may develop black discoloration if it comes in contact with steel. Nail heads that are a black color are usually under the coating surface and will ultimately cause adhesion failure of the topcoat. Once exposed, the nail head will develop red rust.
 

Locate and eliminate the source of moisture. Replace nails with galvanized or other non-rusting nails. Rusty nails that cannot be removed must be sanded to shiny metal, countersunk, coated with a rust-preventive primer and then caulked. Repair moisture damage by sanding weathered wood to a fresh surface.