To reproduce:
Push "Show row indexes" button.
Initial root state is "collapsed", so other items are invisible.
But get row doesn't return -1 for them.


import com.sun.javafx.runtime.VersionInfo;
import javafx.application.Application;
import javafx.beans.property.SimpleIntegerProperty;
import javafx.beans.property.SimpleStringProperty;
import javafx.beans.value.ObservableValue;
import javafx.event.ActionEvent;
import javafx.event.EventHandler;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.control.TreeItem;
import javafx.scene.control.TreeTableColumn;
import javafx.scene.control.TreeTableColumn.CellDataFeatures;
import javafx.scene.control.TreeTableView;
import javafx.scene.layout.HBox;
import javafx.stage.Stage;
import javafx.util.Callback;

public class JavaFXApplication6 extends Application {

    TreeTableView<Person> treeTableView;

    @Override
    public void start(Stage primaryStage) {

        initTreeTableView();

        HBox root = new HBox(10.0);
        root.getChildren().add(treeTableView);

        Button btnRowInd = new Button("Show row indexes");
        btnRowInd.setOnAction(new EventHandler<ActionEvent>() {
            @Override
            public void handle(ActionEvent t) {
                TreeItem<Person> r = treeTableView.getRoot();
                int row = treeTableView.getRow(r);
                System.out.println(r.getValue().firstName + "; row = " + row);
               showTreeItemRowIndex(r);
            }
            
            private void showTreeItemRowIndex(TreeItem<Person> r) {
                for (TreeItem<Person> item : r.getChildren()) {
                     int row = treeTableView.getRow(item);
                    System.out.println(item.getValue().firstName + "; row = " + row);
                    showTreeItemRowIndex(item);
                }
            }
        });

        root.getChildren().add(btnRowInd);

        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() {
        treeTableView = new TreeTableView<>();
        treeTableView.setMinSize(200, 150);
        treeTableView.setPrefSize(250, 200);
        treeTableView.setMaxSize(300, 250);
        treeTableView.setColumnResizePolicy(TreeTableView.CONSTRAINED_RESIZE_POLICY);

        TreeItem<Person> root = new TreeItem<>(new Person("John Smith", 32));
        treeTableView.setRoot(root);
        treeTableView.showRootProperty().set(true);

        final TreeTableColumn<Person, String> firstNameCol = new TreeTableColumn<>("First name");
        firstNameCol.setCellValueFactory(new Callback<TreeTableColumn.CellDataFeatures<Person, String>, ObservableValue<String>>() {
            @Override
            public ObservableValue<String> call(TreeTableColumn.CellDataFeatures<Person, String> p) {
                return p.getValue().getValue().firstName;
            }
        });

        TreeTableColumn<Person, Number> ageCol = new TreeTableColumn<>("Age");
        ageCol.setCellValueFactory(new Callback<TreeTableColumn.CellDataFeatures<Person, Number>, ObservableValue<Number>>() {
            @Override
            public ObservableValue<Number> call(CellDataFeatures<Person, Number> p) {
                return p.getValue().getValue().age;
            }
        });
        treeTableView.getColumns().addAll(firstNameCol, ageCol);

        Person p = new Person("Angela Davis", 33);
        treeTableView.getRoot().getChildren().add(new TreeItem<>(p));

        p = new Person("John Malkovich", 100);
        treeTableView.getRoot().getChildren().add(new TreeItem<>(p));
        
        for (int i = 0; i < 19; i++) {
            p = new Person("Item - " + i, 100);
            treeTableView.getRoot().getChildren().add(new TreeItem<>(p));
        }
    }
}

class Person {

    public final SimpleStringProperty firstName;
    public final SimpleIntegerProperty age;

    public Person(String name, int age) {
        this.firstName = new SimpleStringProperty(name);
        this.age = new SimpleIntegerProperty(age);
    }
}