ADDITIONAL SYSTEM INFORMATION :
macOS High Sierra 10.13.6
Java 1.8.0_181

A DESCRIPTION OF THE PROBLEM :
This happens when two or more JavaFX Windows are on screen.
Eg. assume we have Window 1, Window 2.
We show an Alert with Window 1 as it's owner.
When the Alert is dismissed, the focus incorrectly goes to Window 2, not Window 1 which was the owner of the Alert.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
Run the supplied test program.
Click on the button.
Observe that focus goes to the wrong window.

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
Focus should go to the Window which is the owner of the Alert.
ACTUAL -
Focus goes to the window which isn't the owner of the Alert.

---------- BEGIN SOURCE ----------
import javafx.application.Application;
import javafx.event.ActionEvent;
import javafx.event.EventHandler;
import javafx.scene.Scene;
import javafx.scene.control.Alert;
import javafx.scene.control.Alert.AlertType;
import javafx.scene.control.Button;
import javafx.scene.layout.StackPane;
import javafx.stage.Stage;
 
public class HelloWorld extends Application {
    public static void main(String[] args) {
        launch(args);
    }
    
    @Override
    public void start(
        Stage primaryStage)
    {
        System.out.println("JRE: " + "Platform: " + System.getProperty("java.version"));
        createWindow1(primaryStage);
        createWindow2(primaryStage);
    }
    
    private void createWindow1(
        Stage stage)
    {
        stage.setTitle("Hello World!");
        Button btn = new Button();
        btn.setText("Show Alert");
        btn.setOnAction(new EventHandler<ActionEvent>()
        {
            @Override
            public void handle(ActionEvent event)
            {
                showAlert(stage);
            }
        });
        
        StackPane root = new StackPane();
        root.getChildren().add(btn);
        stage.setScene(new Scene(root, 300, 250));
        stage.show();
    }
    
    private void showAlert(
        Stage primaryStage)
    {
        Alert alert = new Alert(AlertType.CONFIRMATION);
        alert.initOwner(primaryStage);
        alert.show();
    }

    private void createWindow2(
        Stage stage1)
    {
        Stage stage = new Stage();
        stage.setX(stage1.getX() + 300);
        stage.setY(stage1.getY());
        
        stage.setTitle("Hello World!");
        StackPane root = new StackPane();
        stage.setScene(new Scene(root, 300, 250));
        stage.show();
    }
    
}
---------- END SOURCE ----------

FREQUENCY : always