1. LinearGradient and RadialGradient are not rendered correctly.
2. If SubScene's parent has a Background set then SubScene receives mouse events only if SubScene.setFill() is set with a Paint object.

package jiraissue;

import javafx.application.Application;
import javafx.event.EventHandler;
import javafx.scene.Group;
import javafx.scene.PerspectiveCamera;
import javafx.scene.PointLight;
import javafx.scene.Scene;
import javafx.scene.SubScene;
import javafx.scene.input.MouseEvent;
import javafx.scene.layout.Background;
import javafx.scene.layout.BackgroundFill;
import javafx.scene.layout.BorderPane;
import javafx.scene.paint.Color;
import javafx.scene.paint.CycleMethod;
import javafx.scene.paint.LinearGradient;
import javafx.scene.paint.RadialGradient;
import javafx.scene.paint.Stop;
import javafx.scene.shape.Cylinder;
import javafx.stage.Stage;
import javafx.stage.WindowEvent;

public class SubSceneSetFill extends Application {
    
    public static void main(String[] args) {
        launch(args);
    }
    @Override public void start(Stage stage) {
        
        // SubScene

        final Group subSceneRoot = new Group();
        final SubScene subScene = new SubScene(subSceneRoot, 800, 800, true, false);
        
        final Stop[] stopsLG = new Stop[] {new Stop(0.0, Color.rgb(0, 73, 255)),
                                           new Stop(0.7, Color.rgb(127, 164, 255)),
                                           new Stop(1.0, Color.rgb(0, 73, 255))};
        final LinearGradient lg = new LinearGradient(0, 0, 0, 1, true, CycleMethod.NO_CYCLE, stopsLG);
        
        final Stop[] stopsRG = new Stop[]{new Stop(0.0, Color.LIGHTGRAY),
                                          new Stop(0.2, Color.BLACK),
                                          new Stop(1.0, Color.BLACK)};
        final RadialGradient rg = new RadialGradient(0, 0, 0.5, 0.5, 1, true, CycleMethod.NO_CYCLE, stopsRG);

        // Case 1. LinearGradient : strange position
// subScene.setFill(rg);
        
        // Case 2. if SubScene's parent has a Background set
        // then SubScene receives mouse events only if
        // SubScene.setFill() is set with TRANSPARENT, an opaque Color, or Gradient
// subScene.setFill(Color.YELLOWGREEN);
      
        // Test mouse events
        subScene.setOnMousePressed(new EventHandler<MouseEvent>() {
            @Override public void handle(MouseEvent event) {
                System.out.println("OnMousePressed = " + event);
            }
        });

        // Viewing : Camera & Light
        
        // SubScene's camera
        final PerspectiveCamera perspectiveCamera = new PerspectiveCamera(true);
        perspectiveCamera.setFarClip(25);
        perspectiveCamera.setNearClip(0.1);
        perspectiveCamera.setFieldOfView(44);
        
        subScene.setCamera(perspectiveCamera);
       
        // SubScene's light
        final PointLight pointLight = new PointLight(Color.WHITE);
        pointLight.setTranslateZ(-20000);
          
        // Viewing group: camera and headlight
        final Group viewingGroup = new Group(perspectiveCamera, pointLight);
        viewingGroup.setTranslateZ(-5);
        
        // 3D model
        Cylinder cylinder = new Cylinder();
        
        subSceneRoot.getChildren().addAll(cylinder, viewingGroup);
        
        // Scene
        
        // SubScene's parent
        final BorderPane borderPane = new BorderPane();
        borderPane.setMinHeight(0);
        borderPane.setMinWidth(0);
        borderPane.setCenter(subScene);
        
        // Background
        borderPane.setBackground(new Background(new BackgroundFill(Color.YELLOW, null, null)));
           
        final Scene scene = new Scene(borderPane, 850, 850, true);
       
        stage.setOnCloseRequest(new EventHandler<WindowEvent>() {
            @Override public void handle(WindowEvent event) {
                System.exit(0);
            }
        });
        stage.setScene(scene);
        stage.setTitle("SubSceneSetFill");
        
        stage.show();
    }
}