ADDITIONAL SYSTEM INFORMATION :
First hit this problem on Windows 10 with Oracle SE 8. Tried it on Windows 10 with OpenJDK 8 - same. Tried on OpenJDK/OpenJFX13 on Linus - same. AS per reporting bug instructions I tried on OpenJDK/OpenJFX 14ea on WIndows 10 - same.

A DESCRIPTION OF THE PROBLEM :
Creating a simple scene with a fill and the fill is overlayed if a javafx.scene.control is INSTANTIATED - it does not need to be added to the scene to cause the issue

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
Create a StackPane with Rectangle and Text objects and place in VBox. Add VBox to scene with a fill e.g. BLUE.
Add the StackPane to the VBox. Add a mouse click event handler to just Instantiate a javafx.scene.control (e.g. Label)


EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
Show the stage and all is fine - background is filled BLUE and shows a box with text. Any click will not alter the screen

ACTUAL -
When clicking to fire the event the fill is overlayed with a white/grey backround

---------- BEGIN SOURCE ----------
package application;

import javafx.application.Application;
import javafx.stage.Stage;
import javafx.scene.Scene;
import javafx.scene.control.Label;
import javafx.scene.layout.Background;
import javafx.scene.layout.BackgroundFill;
import javafx.scene.layout.StackPane;
import javafx.scene.layout.VBox;
import javafx.scene.paint.Color;
import javafx.scene.shape.Rectangle;
import javafx.scene.text.Font;
import javafx.scene.text.Text;

public class BasicTest extends Application {

private int count = 0;

@Override
public void start(Stage primaryStage) {

Rectangle r = new Rectangle();
r.setWidth(200);
r.setHeight(50);
r.setFill(Color.BLUE);
r.setStroke(Color.WHITE);
r.setStrokeWidth(2);

Text t = new Text();
        t.setText("Confirm");
        t.setFill(Color.WHITE);
        t.setFont(Font.font("null", 40));

StackPane sp = new StackPane(r);
sp.getChildren().add(t);
sp.setMaxWidth(200);

t.setTranslateY(-2);
        
VBox vb = new VBox(sp);

r.setOnMouseClicked(event -> {
if (count == 0) new Label();
else vb.setBackground(new Background(new BackgroundFill(Color.BLUE, null, null)));
count++;});
        
Scene scene = new Scene(vb, 300, 200, Color.BLUE);

primaryStage.setScene(scene);
primaryStage.show();
}

public static void main(String[] args) {
System.out.println("Start");
launch(args);
}
}

---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
There are two workarounds I've found.
1. Use CSS to set the background colour of the scene:
.root {
    -fx-background-color: blue;
}
2. Add a background colour to the VBox:
vb.setBackground(new Background(new BackgroundFill(Color.BLUE, null, null)))

FREQUENCY : always