Rusted hot dip galvanized bolt and nuts

A. The threads in the nut will not be galvanized,because of which you are seeing the rust,as such if the galvanized coating is intact there should not be any problem.

Regards,

A. Mr. Othman,

The problem is that you use HDG coating on bolts and nuts. HDG is traditionally used for this type of coating even though it is not appropriate to use in such application. As Mr. Ameen said, the problem is in the treads of the bolts as well as the nuts. Additionally, most HDG coatings will get scraped off when you drive the bolt into the nut. I suggest you look into different methods of heavy coatings, such as zinc thermo diffusion coating.
Best,

A. Hot dip galvanizing has been used extensively for nuts and bolts for many decades in many countries very successfully. It is not reasonable to say it is an "inappropriate" coating.

You say rust is visible but the measured thickness of the zinc coating appears to show it as still galvanized?
Several possibilities exist.
1. You are not measuring zinc. Perhaps you are using a device to measure the coating thickness that relies on the magnetic properties of the steel, and actually measures the distance from the probe to the steel. In this case its possible to get a false reading from any non ferrous material between probe and steel. Even corrosion products will do this.

2. The rust is on top of the zinc. In this case the rust is staining from elsewhere, and stains the surface of the zinc. This is a common phenomenon, with end users complaining of rust where what they actually have is rust staining on galvanizing. Try scraping the rust with a pen-knife. Do you see shiny zinc underneath?