If I upload my KML file, which contains polygons and pins, to Google Maps, then most of the polygons are missing (see below).

To try and address this, I pasted the kml url to the Google Maps search bar and all of the polygons are now shown on the map but all the pins are missing (see below).

What should I modify in the KML source to have all polygons and pins in the same map?

The issue is outerBoundaryIs in the KML

"KML allows you to create Polygons with holes by designating an outer and inner boundary"

Google Earth Supports this but Google Maps API will not support this data type. It has to to be single Polygon (not multiple-part or donut polygons).

How did you create your kml? According to the Galdos KML Validator (http://kmlvalidator.com/validate.htm), your kml file is not valid:

Unable to read content from the file. Is this one of the supported file types?

However in my PC (ie. Google Earth) it displays correctly (apparently):

and same area without it: