Specs:

System:         Kubuntu 20.04 (Debian family, KDE desktop manager)
JavaFX version: 17.0.1
Eclipse:        2022-03
JVM:            Temurin 11 (OpenJDK)

How to reproduce:

1. Add an event for some Combobox (code below is whole-class example)

   public class Main extends Application {
   public static void main(String[] args) {
       launch(args);
   }
   
   @Override
   public void start(Stage primaryStage) throws Exception {
       ComboBox<Integer> combo = new ComboBox<>();
       combo.getItems().addAll(1, 2, 3);
       combo.setOnAction(new EventHandler<ActionEvent>() {
           @Override
           public void handle(ActionEvent event) {
               System.out.println("test");
           }
       });
       Scene scene = new Scene(new VBox(combo));
       primaryStage.setScene(scene);
       primaryStage.setWidth(400);
       primaryStage.setHeight(400);
       primaryStage.show();
     }
   }
   

2. Add breakpoint inside that event method (handle).

3. Start the JavaFX application from Eclipse in debug mode.

4. Select something from Combobox, so the event is fired.

5. Feel that you can not click on anything (In whole OS. Not just application, which is expected when there is breakpoint and execution stop)

All I can do is start System Manager using the keyboard and kill that application. Have not tried on another Linux. This might happen only on Kubuntu or KDE desktop manager or using only the specs above.