Here's a jsbin demonstrating the issue:
https://jsbin.com/bafewapela/edit?html,console,output

The GeoJSON spec states that features may have a top-level id property:

If a feature has a commonly used identifier, that identifier should be included as a member of the feature object with the name "id".

However, when I have a source with such a feature:

var markers = {
    "type": "FeatureCollection",
    "features": [{
        "id": "my-feature-id",  // <--- feature has an ID
        "type": "Feature",
        "properties": {
            "marker-symbol": "theatre",
        },
        "geometry": {
            "type": "Point",
            "coordinates": [-77.038659, 38.931567]
        }
    }]
};

add it to the map and then get features back via queryRenderedFeatures, the id is gone. The properties and geometry properties are there, but id is not. It would be really helpful if this special property were preserved.

The workaround is to duplicate IDs into properties.id before adding features to the map, but this creates extra work and contradicts the GeoJSON spec.

mapbox-gl-js version: 0.19.1