I've got a part of code, which contains all objects of controllers which I've been using in my program. The topButtonsController is the only one injected from FXML file (fx:include), the others are created by myself. 
I recon that initialize() method is invoked after the constructor of MainController in created, so assuming that all the methods from the initialize() methods should have do their job firstly.
public class MainController {
   @FXML
   private TopButtonsController topButtonsController;
   private AddNewOrderController addNewOrderController = new AddNewOrderController();
   private OrdersController ordersController = new OrdersController();
   @FXML
   private BorderPane borderPane;
   @FXML
   public void initialize() {
       topButtonsController.setMainController(this);
       addNewOrderController.setMainController(this);
       ordersController.setMainController(this);
       System.out.println("Finished injection");    
   }
}
Here I've got a class of controller for another FXML file. After pressing the button the acceptButtonClicked method should invoked, but unfortunately the mainController is Null! Why it is so if I've already set him to a value in MainController initialize method, that should have been hit first. 
public class AddNewOrderController {
   private MainController mainController;
   @FXML
   private TextField nameOfPizzaTextField;
   private ArrayList<Order> arrayList = new ArrayList<Order>();
   private ObservableList<Order> observableList = FXCollections.observableArrayList(arrayList);
   @FXML
   private Button acceptButton;
   @FXML
   void acceptButtonClicked(ActionEvent event) {
       if(mainController == null) {
           System.out.println("MainController is null!!"); //it is printed, why?
       }
       Order order = new Order(nameOfPizzaTextField.getText());
       arrayList.add(order);
       observableList.add(order);
       System.out.println("Dodano "+nameOfPizzaTextField.getText()+"do listy");
       System.out.println(observableList);
       mainController.getOrdersController().getListView().setItems(mainController.getAddNewOrderController().getObservableList()); // here occurs error
   @FXML
   public void initialize() {
   }
   public void setMainController(MainController mainController) {
       this.mainController= mainController;
   }
}
 
    