To resume the issue here is an example code (explanation on bottom):

package example;

import javafx.stage.Stage;
import javafx.scene.Scene;
import javafx.ext.swing.SwingComboBox;
import javafx.ext.swing.SwingComboBoxItem;
import javafx.scene.shape.Rectangle;
import javafx.scene.paint.Color;
import javafx.scene.input.MouseEvent;

var blueColor:Color = Color.BLUE;
var redColor:Color = Color.RED;
var rectangleColor:Color = redColor;

//Changes the color or the rectangle from red to blue and from blue to red
function mousePressed(evt:MouseEvent):Void{
    if (rectangleColor == blueColor){
        rectangleColor = redColor;
    }
        else{
          rectangleColor = blueColor;
    }
}

Stage {
    title: "Application title"
    width: 250
    height: 300
    scene: Scene {
        content: [
            Rectangle{
                height: 20
                width: 200
                y: 45
                x: 3
                fill: bind rectangleColor;
                onMousePressed: mousePressed;
            }
            SwingComboBox{
                items: [
                    SwingComboBoxItem{text:"Item number 1" }
                    SwingComboBoxItem{text:"Item number 2"}
                    SwingComboBoxItem{text:"Item number 3"}
                    SwingComboBoxItem{text:"Item number 4"}
                    SwingComboBoxItem{text:"Item number 5"}
                    SwingComboBoxItem{text:"Item number 6"}
                    SwingComboBoxItem{text:"Item number 7"}
                ]
                selectedIndex: 0
                blocksMouse: true
            }
        ]
    }
}

If you compile and execute this code you can see that if you select the item number 2 from the combobox by clicking your mouse, the rectangle thats behind it will change color due to the onMousePressed event on the rectangle. This doesnt make sense since in the expected behavior the event of the rectangle shouldnt trigger.