A DESCRIPTION OF THE PROBLEM :
Create owner stage and some stages with this owner using Stage.initOwner(). Closing owner stage (which subsequently closes all stages with this owner) causes memory leak.
Closing stage from sub to owner (opposite order) does not cause memory leak.
Affects all current releases Java 10, 9, 8.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
Create and show owner stage. Create and show stage owner set to previous stage. Close owner stage.

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
Both stages are garbage collected.
ACTUAL -
Stages are not garbage collected.

---------- BEGIN SOURCE ----------
import javafx.application.Application;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.control.Label;
import javafx.scene.layout.StackPane;
import javafx.stage.Stage;

public class InitOwnerMemoryLeak extends Application {

    public static void main(String[] args) {
        launch(args);
    }
    
    @Override
    public void start(Stage stage) throws Exception {
        StackPane stackPane = new StackPane();
        Button button = new Button("Run");
        button.setOnMouseClicked(event -> {
            Stage ownerStage = new Stage();
            ownerStage.setTitle("Owner Stage");
            
            StackPane ownerStackPane = new StackPane();
            ownerStackPane.setPrefSize(400, 400);
            
            ownerStage.setScene(new Scene(ownerStackPane));
            ownerStage.show();
            
            Stage subStage = new Stage();
            subStage.setTitle("Sub Stage");
            subStage.initOwner(ownerStage);
            
            StackPane subStackPane = new StackPane();
            subStackPane.setPrefSize(300, 300);
            Label label = new Label("Close my owner to cause memory leak");
            subStackPane.getChildren().add(label);
            
            subStage.setScene(new Scene(subStackPane));
            subStage.show();
        });
        
        stackPane.getChildren().add(button);
        
        stage.setScene(new Scene(stackPane));
        stage.show();
    }
}
---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
For stage which calls Stage.initOwner() call also
Stage.getOwner().addEventFilter(WindowEvent.WINDOW_HIDING, event -> Stage.close());

FREQUENCY : always