To reproduce run following code



import javafx.application.Application;
import javafx.builders.FlowPaneBuilder;
import javafx.builders.PaneBuilder;
import javafx.builders.SplitPaneBuilder;
import javafx.builders.TilePaneBuilder;
import javafx.scene.Parent;
import javafx.scene.Scene;
import javafx.scene.control.SplitPane;
import javafx.scene.layout.VBox;
import javafx.scene.paint.Color;
import javafx.scene.shape.Rectangle;
import javafx.stage.Stage;

public class SplitPanePadding extends Application {

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

    private Parent getContent() {

        VBox list = new VBox();
        list.setManaged(false);
        SplitPane pane = SplitPaneBuilder.create().items(
                TilePaneBuilder.create().children(new Rectangle(40, 40, Color.WHITESMOKE)).build(),
                FlowPaneBuilder.create().children(new Rectangle(40, 40, Color.BLUE)).build(),
                PaneBuilder.create().children(new Rectangle(40, 40, Color.RED)).build())
                .prefWidth(150)
                .prefHeight(150)
                .maxWidth(150)
                .maxHeight(150)
                .build();
        pane.setDividerPositions(0.33, 0.67);
        pane.setFocusTraversable(false);
        pane.setStyle("-fx-border-color:green;");
        pane.setMaxSize(150,150);
        list.getChildren().addAll(pane);
        return list;
    }

    public void start(Stage stage) {
        stage.setX(100);
        stage.setY(100);
        Scene scene = new Scene(getContent(),800,300);
        stage.setScene(scene);
        stage.setVisible(true);
    }
}