The mouse click events on Rectangle are not all caught - the system/runtime seems not to be sensitive/quick
enough to catch such events. On the other hand, for mouse click event on Button, the system/runtime seems to
be sensitive/quick enough to catch every event.

Below codes used to re-produce...

1. Quickly click on one rectangle, then, another, then, another,,,
   You will see NOT all click-event generates output messsage
2. Quickly click on one button, then, another, then, another,,,
   You will see all click-event generates output messsage

--- Code for re-producing ---
import javafx.application.Application;
import javafx.event.ActionEvent;
import javafx.event.EventHandler;
import javafx.scene.Group;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.input.MouseEvent;
import javafx.scene.layout.HBox;
import javafx.scene.paint.Color;
import javafx.scene.paint.Paint;
import javafx.scene.shape.Rectangle;
import javafx.stage.Stage;

/**
 *
 * @author lianqi.li
 */
public class EventIssue extends Application {
    @Override public void start(Stage stage) {
        final Group root = new Group();
        final Scene scene = new Scene(root, 400, 300);
        
        Rectangle[] rects = {new Rectangle(50, 50, Color.RED), new Rectangle(50, 50, Color.YELLOW), new Rectangle(50, 50, Color.BLUE), new Rectangle(50, 50, Color.GREEN)};
        for (int i = 0; i < rects.length; i++) {
            final Paint color = rects[i].getFill();
            final int n = i;
            rects[i].setOnMouseClicked(new EventHandler<MouseEvent>() {
                @Override
                public void handle(MouseEvent event) {
                    System.out.println("Clicked on #" + n + " - " + color);
                }
            });
        }

        Button[] buttons = {new Button("Button1"), new Button("Button2"), new Button("Button3"), new Button("Button4")};
        for (int i = 0; i < buttons.length; i++) {
            final int n = i;
            buttons[i].setOnAction(new EventHandler<ActionEvent>() {
                @Override
                public void handle(ActionEvent event) {
                    System.out.println("Clicked on button" + n);
                }
            });
        }

        HBox hBox1 = new HBox(10);
        hBox1.getChildren().addAll(rects);

        HBox hBox2 = new HBox(10);
        hBox2.getChildren().addAll(buttons);

        hBox1.setTranslateX(50);
        hBox1.setTranslateY(50);
        hBox2.setTranslateX(50);
        hBox2.setTranslateY(250);

        root.getChildren().addAll(hBox1, hBox2);
        
        stage.setScene(scene);
        stage.setVisible(true);
    }

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