Rust spots on metal roof

[Carey]

If it is a very small area (like around the hole where the fastener was), use a very small wire brush or a Japanese rubber & grit "rust eraser for knives" (I slice a pencil shaped piece) for a lot more controlled rust removal that a large wire brush
Rust Reformer type produces are good, but seal them with a coating
& spray the replacement fasteners, if nothing ease a wax-like coating will help (food grade if on catchment)