To reproduce:
Click 'Initialize';
Click 'Set graphic';

import com.sun.javafx.runtime.VersionInfo;
import javafx.application.Application;
import static javafx.application.Application.launch;
import javafx.application.Platform;
import javafx.beans.property.SimpleIntegerProperty;
import javafx.beans.property.SimpleStringProperty;
import javafx.beans.value.ObservableValue;
import javafx.collections.FXCollections;
import javafx.collections.ObservableList;
import javafx.event.ActionEvent;
import javafx.event.EventHandler;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.control.SelectionMode;
import javafx.scene.control.TreeItem;
import javafx.scene.control.TreeTableColumn;
import javafx.scene.control.TreeTableColumn.CellDataFeatures;
import javafx.scene.control.TreeTableView;
import javafx.scene.control.cell.ChoiceBoxTreeTableCell;
import javafx.scene.control.cell.TextFieldTreeTableCell;
import javafx.scene.input.MouseButton;
import javafx.scene.input.MouseEvent;
import javafx.scene.layout.HBox;
import javafx.scene.layout.Pane;
import javafx.scene.paint.Color;
import javafx.scene.shape.Circle;
import javafx.stage.Stage;
import javafx.util.Callback;

public class Main extends Application {
    
    private SimpleIntegerProperty clickCounter = new SimpleIntegerProperty(0);
    private ObservableList<String> idPool = FXCollections.observableArrayList();
    private TreeTableView ttv;
    Pane root;
    
    @Override
    public void start(Stage primaryStage) {
        Button btnInit = new Button("Initialize");
        btnInit.setOnAction(new EventHandler<ActionEvent>() {

            @Override
            public void handle(ActionEvent t) {
                initTreeTableView();
            }
        });
        Button btnSetGraphic = new Button("Set graphic");
        btnSetGraphic.setOnAction(new EventHandler<ActionEvent>() {

            @Override
            public void handle(ActionEvent event) {
                TreeItem parent = ttv.getRoot();
                Circle circle = new Circle(6.75, Color.RED);
                
                ((TreeItem) parent.getChildren().get(0)).setGraphic(circle);
            }
        });
        
        root = new HBox(10.0);
        root.getChildren().addAll(btnInit, btnSetGraphic);
        Scene scene = new Scene(root, 400, 300);
        
        primaryStage.setTitle(VersionInfo.getRuntimeVersion());
        primaryStage.setScene(scene);
        primaryStage.show();
    }

    public static void main(String[] args) {
        launch(args);
    }

    private void initTreeTableView() {
        ttv = new TreeTableView();
        root.getChildren().add(ttv);
        
        ttv.setRoot(new TreeItem(new Main.Data("Root", "42")));
        ttv.getRoot().setExpanded(true);
        
        final TreeTableColumn colName = new TreeTableColumn("Name");
        colName.setCellValueFactory(new Callback<TreeTableColumn.CellDataFeatures<Main.Data, String>, ObservableValue<String>>() {
            @Override
            public ObservableValue<String> call(CellDataFeatures<Main.Data, String> p) {
                return p.getValue().getValue().name;
            }
        });
        
        colName.setMinWidth(100d);
        
        final TreeTableColumn colId = new TreeTableColumn("Id");
        colId.setCellValueFactory(new Callback<TreeTableColumn.CellDataFeatures<Main.Data, String>, ObservableValue<String>>() {
            @Override
            public ObservableValue<String> call(CellDataFeatures<Main.Data, String> p) {
                return p.getValue().getValue().id;
            }
        });
        
        colId.setMinWidth(75d);
        
        ttv.getColumns().addAll(colName, colId);

        ttv.setOnMouseClicked(new EventHandler<MouseEvent>() {
            @Override
            public void handle(MouseEvent t) {
                if (t.getButton() == MouseButton.PRIMARY) {
                    clickCounter.set(clickCounter.get() + 1);
                }
            }
        });

        ttv.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
        ttv.getSelectionModel().setCellSelectionEnabled(true);
        ttv.setEditable(true);
        colName.setCellFactory(TextFieldTreeTableCell.forTreeTableColumn());
        colId.setCellFactory(ChoiceBoxTreeTableCell.forTreeTableColumn(idPool));
        
        Platform.runLater(new Runnable() {
            @Override
            public void run() {
                for (int i = 0; i < 10; i++) {
                    String id = "id - " + i;
                    idPool.add(id);

                    TreeItem treeItem = new TreeItem(new Main.Data("item - " + i, id));
                    ttv.getRoot().getChildren().add(treeItem);

                    for (int j = 0; j < 2; j++) {
                        treeItem.getChildren().add(new TreeItem(new Main.Data("item - " + i + " - " + j, id)));
                    }
                }
            }
        });
    }
    
    private class Data {
        public SimpleStringProperty name;
        public SimpleStringProperty id;
        
        public Data(String _name, String _id) {
            name = new SimpleStringProperty(_name);
            id = new SimpleStringProperty(_id);
        }
    }
}