How about a wider shot of what we are looking at as that is a large expanse of "flashing" from your picture.

Gently rub off the rust with steel wool. If it returns, it's bad zinc plating or the zinc has been knocked off. If it doesn't, it was some sort of rust contamination. There's no fixing it.

Re: "The metal is zinc, which is not supposed to rust."

The 'metal' is actually galvanized steel, which is a zinc layer applied to the surface of the steel sheet either through electroplating or hot dip galvanizing. The intent of the zinc is to be sacrificial in relation to the steel; it is desired that the zinc 'rusts' or oxidizes first and thus protect the steel from rusting. Zinc 'rust' is actually a white product which is considered to be more pleasing to the eye than the red rust of steel. Theoretically, all the zinc oxidizes before the steel begins rusting but this doesn't always happen because galvanic corrosion processes involve the flow of electricity at the atom level and this flow is not always uniform for a variety of manufacturing and environmental factors. The bottom line is that what you see is normal, spots of rust will appear as the galvanized steel ages. If you don't like what you are seeing, paint the surfaces.

@HU-867564120 This is brand new (completed a little over a year ago), so I assume it shouldn't rust for at least a while (5-10 years?). Is it likely it's defective or low-grade material? Is it safe to assume most materials are pretty standard grade? If it is rust, because the zinc plating has worn off the steel, and the steel is rusting, would it be worth asking the contractor to re-do it? It is technically under a 3 year warranty

Is that steel railing? Is there any rust on the railing? On the underside of the railing just above the flashing?

@ci_lantro (great name, love cilantro ;) )

The railing I believe is steel that was painted, and welded to supports that come out of the flashing.