When Ctrl+Clicking a selected item in a table, the item retains a blue border (probably to indicate it is the anchor).
However selectedIndex will remain the value it was, while selectedItem will become null.

The following example demonstrates the problem by displaying two bound checkboxes together with a table. Both checkboxes should always have the same state (since selectedIndex < 0 should be equivalent to selectedItem == null), but they are not, if a selected item is Ctrl-clicked.

import javafx.application.Application;
import javafx.beans.property.SimpleStringProperty;
import javafx.beans.property.StringProperty;
import javafx.beans.value.ObservableValue;
import javafx.collections.FXCollections;
import javafx.collections.ObservableList;
import javafx.scene.Scene;
import javafx.scene.control.CheckBox;
import javafx.scene.control.TableColumn;
import javafx.scene.control.TableView;
import javafx.scene.control.cell.PropertyValueFactory;
import javafx.scene.layout.GridPane;
import javafx.stage.Stage;

public class TableViewHasSelection extends Application {

    ObservableList<Person> items = FXCollections.observableArrayList();
    TableView<Person> table = new TableView<Person>();

    public TableViewHasSelection() {
    }

    @Override
    public void start(Stage primaryStage) throws Exception {
     GridPane grid = new GridPane();
    
    
        table.setItems(items);
        TableColumn<Person, String> firstNameCol = new TableColumn<Person, String>("First Name");
        firstNameCol.setCellValueFactory(new PropertyValueFactory<Person, String>("firstName"));
        TableColumn<Person, String> lastNameCol = new TableColumn<Person, String>("Last Name");
        lastNameCol.setCellValueFactory(new PropertyValueFactory<Person, String>("lastName"));
        table.getColumns().setAll(firstNameCol, lastNameCol);
        table.getSelectionModel().selectedIndexProperty().addListener((ObservableValue<? extends Number> observable, Number oldValue, Number newValue) -> { selectionChanged(); });
        table.getSelectionModel().selectedItemProperty().addListener((ObservableValue<? extends Person> observable, Person oldValue, Person newValue) -> { selectionChanged(); });
        addPersons();
        grid.add(table, 0, 1, 3, 1);
        
        CheckBox cb1 = new CheckBox("selectedIndex < 0");
        cb1.selectedProperty().bind(table.getSelectionModel().selectedIndexProperty().lessThan(0));
        grid.add(cb1, 0, 0);
        
        CheckBox cb2 = new CheckBox("selectedItem.isNull");
        cb2.selectedProperty().bind(table.getSelectionModel().selectedItemProperty().isNull());
        grid.add(cb2, 1, 0);
        
        
        Scene scene = new Scene(grid, 400, 400);
        primaryStage.setScene(scene);
        primaryStage.show();
    }

    // simulate server call, usually this would take sort order property into account
    private void addPersons() {
        for (int i = 0; i < 50; i++) {
            Person p = new Person();
            int idx = items.size();
            p.setFirstName(idx + " John");
            p.setLastName(idx + "Doe");
            items.add(p);
        }
    }

    private void selectionChanged() {
     System.out.println(
     "isEmpty: " + table.getSelectionModel().isEmpty()
     + ", vs. selectedIndex: " + table.getSelectionModel().getSelectedIndex()
     + " vs. item.isNull: " + (table.getSelectionModel().getSelectedItem() == null)
     );
    }

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

    public class Person {
        private StringProperty firstName;

        public void setFirstName(String value) {
            firstNameProperty().set(value);
        }

        public String getFirstName() {
            return firstNameProperty().get();
        }

        public StringProperty firstNameProperty() {
            if (firstName == null)
                firstName = new SimpleStringProperty(this, "firstName");
            return firstName;
        }

        private StringProperty lastName;

        public void setLastName(String value) {
            lastNameProperty().set(value);
        }

        public String getLastName() {
            return lastNameProperty().get();
        }

        public StringProperty lastNameProperty() {
            if (lastName == null)
                lastName = new SimpleStringProperty(this, "lastName");
            return lastName;
        }
    }
}