To reproduce right-click on the scroll bar between the knob and any arrow.
See that the knob moves and context menu appears simultaneously.

import javafx.application.Application;
import javafx.event.EventHandler;
import javafx.scene.Scene;
import javafx.scene.control.ContextMenu;
import javafx.scene.control.Label;
import javafx.scene.control.MenuItem;
import javafx.scene.control.ScrollPane;
import javafx.scene.input.ContextMenuEvent;
import javafx.scene.layout.HBox;
import javafx.scene.layout.VBox;
import javafx.stage.Stage;

public class BugScrollPaneContextMenu extends Application {

    ScrollPane testedControl;

    @Override
    public void start(Stage stage) {

        testedControl = new ScrollPane();
        VBox content = new VBox(15d);
        for (int i = 0; i < 10; i++) {
            content.getChildren().add(new Label("label #" + i));
        }
        testedControl.setContent(content);
        testedControl.setMaxHeight(150d);

        final ContextMenu contextMenu = new ContextMenu();
        for (int i = 0; i < 3; i++) {
            contextMenu.getItems().add(new MenuItem("Menu item - " + i));
        }

        testedControl.setOnContextMenuRequested(new EventHandler<ContextMenuEvent>() {
            @Override
            public void handle(ContextMenuEvent t) {
                contextMenu.show(testedControl, t.getScreenX(), t.getScreenY());
            }
        });

        HBox root = new HBox(20d);
        root.getChildren().add(testedControl);

        Scene scene = new Scene(root, 300, 250);

        stage.setScene(scene);
        stage.setTitle(System.getProperty("java.runtime.version") + "; " + System.getProperty("javafx.runtime.version"));
        stage.show();
    }

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

}