FULL PRODUCT VERSION :
Tested on several different versions, all gives the same result:
JDK 8.0.131 (on Windows)
JDK 8.0.172 (early access, on Windows)
JDK 9.0.4 (on Windows)
OpenJDK 8.0.151 and OpenJFK 8.0.60 (Ubuntu 16.04 inside VirtualBox)

ADDITIONAL OS VERSION INFORMATION :
Microsoft Windows [Version 10.0.16299.309]
Linux stekeblad-VirtualBox 4.13.0-37-generic #42~16.04.1-Ubuntu SMP Wed Mar 7 16:03:28 UTC 2018 x86_64 x86 64 GNU/Linux

EXTRA RELEVANT SYSTEM CONFIGURATION :
Executed from inside IntelliJ IDEA 2017.3.5 (Community Edition)

A DESCRIPTION OF THE PROBLEM :
Calling toolbar.getChildrenUnmodifiable() on a ToolBar with one or more items in it (eg. buttons) returns no results and when calling button.getParent().getId() on a Button inside a ToolBar generates a NullPointerException.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
Create a simple JavaFx application with a ToolBar and a button inside the ToolBar.
Give both of them Ids.
In the controller try call getParent().getId() on the button and check the returned result of getChildrenUnmodifiable() on the ToolBar

Code for a JavaFx controller class and a window fxml file is attached in the code section, a Main class and the imports for the Controller is not included to keep it short.

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
Expected output of the attached code:
Window is AnchorPane[id=window]
Toolbar is ToolBar[id=toolbar, styleClass=tool-bar]
Button_Toolbar is Button[id=button_toolbar, styleClass=button]'Button'
Button_Window is: Button[id=button_window, styleClass=button]'Button'

The id of the button_toolbar's parent is: toolbar
The id of the button_window's parent is: window
The id of the toolbar's parent is: window

The ids of the toolbar's children is:
- button_toolbar
The ids of the window's children is:
- toolbar
- button_window
ACTUAL -
Window is AnchorPane[id=window]
Toolbar is ToolBar[id=toolbar, styleClass=tool-bar]
Button_Toolbar is Button[id=button_toolbar, styleClass=button]'Button'
Button_Window is: Button[id=button_window, styleClass=button]'Button'

Actual output of the attached code:
Failed finding parent of button_toolbar
The id of the button_window's parent is: window
The id of the toolbar's parent is: window

The ids of the toolbar's children is:
The ids of the window's children is:
- toolbar
- button_window

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------
public class Controller implements Initializable {

    public ToolBar toolbar;
    public Button button_toolbar;
    public Button button_window;
    public AnchorPane window;

    @Override
    public void initialize(URL location, ResourceBundle resources) {
        System.out.println("Window is " + window); // null checks
        System.out.println("Toolbar is " + toolbar);
        System.out.println("Button_Toolbar is " + button_toolbar);
        System.out.println("Button_Window is: " + button_window + "\n");

        try { // Try get the parent of the button_toolbar
            System.out.println("The id of the button_toolbar's parent is: " + button_toolbar.getParent().getId());
        } catch (Exception e) {
            System.out.println("Failed finding parent of button_toolbar");
        }
        try { // Try get the parent of the button_window
            System.out.println("The id of the button_window's parent is: " + button_window.getParent().getId());
        } catch (Exception e) {
            System.out.println("Failed finding parent of button_window");
        }
        try { // Try get the parent of the toolbar
            System.out.println("The id of the toolbar's parent is: " + toolbar.getParent().getId());
        } catch (Exception e) {
            System.out.println("Failed finding parent of toolbar");
        }

        // Try get the children of the toolbar
        System.out.println("\nThe ids of the toolbar's children is: ");
        for (Node child : toolbar.getChildrenUnmodifiable()) {
            System.out.println("- " + child.getId());
        }
        // Try get children of window
        System.out.println("The ids of the window's children is: ");
        for (Node child : window.getChildrenUnmodifiable()) {
            System.out.println("- " + child.getId());
        }
    }
}

<?xml version="1.0" encoding="UTF-8"?>

<?import javafx.scene.control.Button?>
<?import javafx.scene.control.ToolBar?>
<?import javafx.scene.layout.AnchorPane?>

<AnchorPane fx:id="window" prefHeight="400.0" prefWidth="600.0" xmlns="http://javafx.com/javafx/8.0.111" xmlns:fx="http://javafx.com/fxml/1" fx:controller="Controller">
   <children>
      <ToolBar fx:id="toolbar" layoutX="29.0" layoutY="14.0" prefHeight="40.0" prefWidth="200.0" AnchorPane.leftAnchor="0.0" AnchorPane.rightAnchor="0.0" AnchorPane.topAnchor="0.0">
        <items>
          <Button fx:id="button_toolbar" mnemonicParsing="false" text="Button" />
        </items>
      </ToolBar>
      <Button fx:id="button_window" layoutX="14.0" layoutY="40.0" mnemonicParsing="false" text="Button" />
   </children>
</AnchorPane>
---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
Access the Nodes inside the toolbar directly instead of through the toolbar