Scene can shrink to 2-pixel size when it contains an empty group or a non-empty group which resizes itself with changes to scene size (using ChangeListener or InvalidationListener).

To reproduce, run the following application (you can modify it to try different cases):

import javafx.application.Application;
import javafx.beans.value.ChangeListener;
import javafx.beans.value.ObservableValue;
import javafx.scene.Scene;
import javafx.scene.layout.Pane;
import javafx.scene.paint.Color;
import javafx.scene.shape.Rectangle;
import javafx.stage.Stage;

public class Main extends Application {

    @Override
    public void start(Stage stage) {
        //Rectangle r = new Rectangle(100, 100, Color.ALICEBLUE);
        Pane box = new Pane();
        box.setStyle("-fx-border-color: red;");
        //box.getChildren().add(r);
        Scene scene = new Scene(box);
        
        scene.widthProperty().addListener(new ChangeListener<Number>() {
            @Override
            public void changed(ObservableValue<? extends Number> ov, Number t, Number t1) {
                System.out.println("Scene width changed from " + t + " to " + t1);
                //box.setPrefWidth((double) t1);
            }
        });

        scene.heightProperty().addListener(new ChangeListener<Number>() {
            @Override
            public void changed(ObservableValue<? extends Number> ov, Number t, Number t1) {
                System.out.println("Scene height changed from " + t + " to " + t1);
                //box.setPrefHeight((double) t1);
            }
        });
        
        stage.widthProperty().addListener(new ChangeListener<Number>() {
            @Override
            public void changed(ObservableValue<? extends Number> ov, Number t, Number t1) {
                System.out.println("Stage width changed from " + t + " to " + t1);
            }
        });

        stage.heightProperty().addListener(new ChangeListener<Number>() {
            @Override
            public void changed(ObservableValue<? extends Number> ov, Number t, Number t1) {
                System.out.println("Stage height changed from " + t + " to " + t1);
            }
        });
        
        stage.setScene(scene);
        stage.setWidth(800);
        stage.setHeight(600);
        stage.sizeToScene();
        stage.show();
    }
}