An standard Error Alert created with: new Alert(Alert.AlertType.ERROR); can be dismissed by pressing the close button in addition to "OK". However if you add a custom button, like I have in the example below, the close button no longer functions.

Test case: (attaching the file to this issue failed with "missing token")

package example;

import javafx.application.Application;
import javafx.scene.control.Alert;
import javafx.scene.control.ButtonType;
import javafx.scene.control.TextArea;
import javafx.scene.layout.Priority;
import javafx.scene.layout.VBox;
import javafx.stage.Stage;

public class AlertBug extends Application {

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

@Override
public void start(Stage stage) throws Exception {
showAlertDialog("Alert Close Bug", "The close button doesn't work",
"When the extra button is added below the close button at the top doesn't work.\n"
+ "Edit the source to turnoff the addition of the \"Copy to clipboard\" button\n"
+ "and the close button up there ^^^ will work."
);
}

private void showAlertDialog(String title, String header, String details) {
Alert alert = new Alert(Alert.AlertType.ERROR);
alert.setTitle(title);
alert.setHeaderText(header);

// Use a scrollable area for the details
TextArea textarea = new TextArea();
textarea.setEditable(false);
textarea.setMaxSize(Double.MAX_VALUE, Double.MAX_VALUE);
VBox.setVgrow(textarea, Priority.ALWAYS);
textarea.setText(details);
alert.getDialogPane().setContent(textarea);
alert.setResizable(true);

// Add a button to copy details to clipboard
// Set to false and the close button on the Alert starts to work.
if (true) {
ButtonType copyTo = new ButtonType("Copy to clipboard");
alert.getButtonTypes().add(copyTo);
}

alert.showAndWait();
}
}