If I use a TilePane, I recognized a extra space added to its container.

Run this code: (and replace the tilePane by the hBox in the root.getChildren collection, to see the difference).

import javafx.application.Application;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.layout.HBox;
import javafx.scene.layout.TilePane;
import javafx.scene.layout.VBox;
import javafx.stage.Stage;

public class TestApp3 extends Application {

    public static void main(String[] args) {
        Application.launch(args);
    }

    public void start(final Stage stage) throws Exception {

        VBox root = new VBox();

        TilePane tilePane = new TilePane();
        tilePane.getChildren().addAll(new Button(), new Button());

        HBox hBox = new HBox();
        hBox.getChildren().addAll(new Button(), new Button());

        root.getChildren().addAll(tilePane, new Button("Below this Button is a free space"));
        Scene scene = new Scene(root);
        stage.setScene(scene);
        stage.show();
    }
}