To reproduce:
1. Push 'Add item'
2. Open and close combobox
3. Push 'Set placeholder'
4. Push 'Remove all'
5. Open combobox

Result: it will be rendered outside of the parent pane

import com.sun.javafx.runtime.VersionInfo;
import javafx.application.Application;
import javafx.event.ActionEvent;
import javafx.event.EventHandler;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.control.ComboBox;
import javafx.scene.control.Label;
import javafx.scene.layout.HBox;
import javafx.scene.layout.Pane;
import javafx.scene.layout.VBox;
import javafx.scene.paint.Color;
import javafx.scene.shape.Circle;
import javafx.stage.Stage;

public class ComboBoxAppWithPlaceholder extends Application {
    public static void main(String[] args) {
        launch(args);
    }

    @Override
    public void start(Stage stage) throws Exception {
        stage.setTitle(VersionInfo.getRuntimeVersion());
        stage.setScene(createScene());

        stage.show();
    }

    private Scene createScene() {
        final ComboBox comboBox = new ComboBox();

        Button addItem = new Button("Add item");
        addItem.setOnAction(new EventHandler<ActionEvent>() {
            int i;
            @Override
            public void handle(ActionEvent actionEvent) {
                comboBox.getItems().add("Item " + i++);
            }
        });

        Button remove = new Button("Remove all");
        remove.setOnAction(new EventHandler<ActionEvent>() {
            @Override
            public void handle(ActionEvent actionEvent) {
                comboBox.getItems().clear();
            }
        });

        Button setPlaceHolder = new Button("Set placeholder");
        setPlaceHolder.setOnAction(new EventHandler<ActionEvent>() {
            @Override
            public void handle(ActionEvent actionEvent) {
                comboBox.setPlaceholder(new Circle(12, Color.RED));
            }
        });

        HBox root = new HBox();

        Pane pane = new Pane();
        pane.setPrefSize(220, 220);
        pane.setMinSize(220, 220);
        pane.setStyle("-fx-border-color: PALEGREEN");
        pane.getChildren().add(comboBox);

        root.getChildren().add(new VBox(pane, addItem, remove, setPlaceHolder));
        root.getChildren().add(new VBox(new Label("Stub")));

        return new Scene(root, 400, 300);
    }
}