You can run an attached code to reproduce:

import javafx.application.Application;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.control.ProgressIndicator;
import javafx.scene.control.ToggleButton;
import javafx.scene.layout.HBox;
import javafx.stage.Stage;

public class JavaApplication50 extends Application {

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

    @Override
    public void start(Stage stage) throws Exception {
        HBox hb = new HBox();
        hb.setPrefSize(300, 300);

        hb.getChildren().addAll(new Button("Button"), new ProgressIndicator(0.5), new ToggleButton("tbutton"));

        hb.setStyle("-fx-border-color: RED;");

        Scene scene = new Scene(hb, 400, 400);
        stage.setScene(scene);
        stage.show();
    }
}

Look at the attached image.

Controls are in HBox, and progress indicator doesn't fit into common "line" in different alignments.