When entering fullscreen mode on MacOS, dialogs/alerts are not shown correctly. 
Instead a separate tab is opened where the content of the dialog is shown.

The following example program shows the problem:

package prv.rli.codetest;

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.ButtonBar.ButtonData;
import javafx.scene.control.ButtonType;
import javafx.scene.control.Menu;
import javafx.scene.control.MenuBar;
import javafx.scene.control.MenuItem;
import javafx.scene.input.KeyCombination;
import javafx.scene.layout.VBox;
import javafx.stage.Stage;

public class DialogConfirmDangerousAction extends Application {

    public DialogConfirmDangerousAction() {
    }

    @Override
    public void start(Stage stage) throws Exception {
        stage.setTitle("Dialog default button");
        Scene scene = new Scene(new VBox(), 400, 350);
 
        MenuBar menuBar = new MenuBar();
 
        // --- Menu File
        Menu menuFile = new Menu("File");
        menuBar.getMenus().addAll(menuFile);
        
        MenuItem test = new MenuItem("Open Dialog");
        test.setAccelerator(KeyCombination.keyCombination("Ctrl+O"));
        test.setOnAction(new EventHandler<ActionEvent>() {
            public void handle(ActionEvent t) {
        		Alert alert = new Alert(AlertType.CONFIRMATION);
        		alert.setTitle("Really");
        		alert.setHeaderText("Danger, Will Robinson");
        		alert.setContentText("This will make the universe collapse. Are you sure?");
        		ButtonType yes = new ButtonType("Yes", ButtonData.OTHER);
        		ButtonType no = new ButtonType("No", ButtonData.CANCEL_CLOSE);
        		alert.getButtonTypes().setAll(no, yes);
            	alert.showAndWait();            	
            }
        });                
        
        menuFile.getItems().add(test);
 
        ((VBox) scene.getRoot()).getChildren().addAll(menuBar);
 
        stage.setScene(scene);
        stage.show();    
    }
    
    public static void main(String[] args) {
        launch(args);
    }
}

If it is started, fullscreen mode is entered and the menu item activated, the dialog is shown as described above.