Download File using PHP

create a new download.php? Download = filename
at the beginning of the file we place a session_start ();
then

   <?php
session_start();
   include "includes/functions.php";
   if(isset($_GET['descarga'])) {
    descargar($filename);
    }
    ?>

in the first:

<?php
//para que el nombre siempre quede guardo
session_start();

//set it to writable location, a place for temp generated PNG files
 $PNG_TEMP_DIR = dirname(__FILE__).DIRECTORY_SEPARATOR.'php_action'.DIRECTORY_SEPARATOR.'temp'.DIRECTORY_SEPARATOR;

//html PNG location prefix
$PNG_WEB_DIR = 'temp/';

include "phpqrcode/qrlib.php";

//ofcourse we need rights to create temp dir
if (!file_exists($PNG_TEMP_DIR))
mkdir($PNG_TEMP_DIR);


$filename = $PNG_TEMP_DIR.'test.png';

//processing form input
//remember to sanitize user input in real-life solution !!!
$errorCorrectionLevel = 'L';
if (isset($_REQUEST['level']) && in_array($_REQUEST['level'], 
array('L','M','Q','H')))
$errorCorrectionLevel = $_REQUEST['level'];

$matrixPointSize = 4;
if (isset($_REQUEST['size']))
$matrixPointSize = min(max((int)$_REQUEST['size'], 1), 10);


if (isset($_REQUEST['data'])) {

//it's very important!
if (trim($_REQUEST['data']) == '')
    die('Introduzca la Referencia del Producto en el campo "Referencia" 
y haga clic en "Generar", no puede dejar en blanco los datos! <a href="?">Regresar</a>');
  $ReferenciaProducto = $_REQUEST['data'];
// user data
$filename = $PNG_TEMP_DIR.$ReferenciaProducto.'-'.md5($_REQUEST['data'].'|'.$errorCorrectionLevel.'|'.$matrixPointSize).'.png';
$_SESSION["filename"] = $filename;
QRcode::png($_REQUEST['data'], $filename, $errorCorrectionLevel, $matrixPointSize, 2);

} else {

 //default data
echo 'La Imagen QR que aparece por defecto, es de prueba, hasta que no introduzca la referncia en el campo inferior y presione "Generar" no se visualizará la imagen definitiva"<hr/>';
QRcode::png('PHP QR Code :)', $filename, $errorCorrectionLevel, $matrixPointSize, 2);

  }

 //display generated file
// echo '<img src="'.$PNG_WEB_DIR.basename($filename).'" /><hr/>';
 echo '<img src="'.'php_action'.DIRECTORY_SEPARATOR.$PNG_WEB_DIR.basename($filename).'" /><hr/>';

//.'php_action'.DIRECTORY_SEPARATOR.

//config form
echo '<form action="show_product2.php" method="post">
Ref:&nbsp;<input name="data" value="'.(isset($_REQUEST['data'])? 
htmlspecialchars($_REQUEST['data']):'Escriba  Ref.de Producto').'" />&nbsp;
Definición:&nbsp;<select name="level">
    <option value="L"'.(($errorCorrectionLevel=='L')?' selected':'').'>L 
- Muy Baja</option>
    <option value="M"'.(($errorCorrectionLevel=='M')?' selected':'').'>Baja</option>
    <option value="Q"'.(($errorCorrectionLevel=='Q')?' selected':'').'>Media</option>
    <option value="H"'.(($errorCorrectionLevel=='H')?' selected':'').'>Alta - La Mejor</option>
</select>&nbsp;
Tamaño:&nbsp;<select name="size">';

 for($i=1;$i<=10;$i++)
echo '<option value="'.$i.'"'.(($matrixPointSize==$i)?' selected':'').'>'.$i.'</option>';

echo '</select>&nbsp;
<input type="submit" value="GENERAR"></form><hr/>';


?>
  <center>        


   <?php
//validamos que el nombre del archivo exista en la varible de session

   if(isset($_SESSION["filename"])) {
      echo "<form method='get' action='download.php?descarga='".$_SESSION["filename"].">";

echo' <button class="btn btn-default button3" data-toggle="submit" 
name="Descargar" data-target = "Descarga"><i class="glyphicon glyphicon- 
  download-alt"></i> Descargar Qr en su Computadora </button>

  &nbsp;<button class="btn btn-default button3" data-toggle="submit" 
id="GuardarQRlBtn" data-target="#GuardarQRlBtn"> <i class="glyphicon 
glyphicon-tasks"></i> Guardar Qr en el Servidor </button></form>';
    ?>
</center>

When you press the Download button, the form that includes it is launched, and it takes you to the same file that you are running. The entire page is being reloaded, and although at that moment Descargar is defined, the file headers that you have in the download () function are NOT SENT, since the html forms that make up your web page have already been sent.

I suggest 2 ways:

That the action to download is in another file:

generates a file (eg: downloadQr.php ) with the following content:

<?php
  include "includes/functions.php";
  $PNG_TEMP_DIR = dirname(__FILE__).DIRECTORY_SEPARATOR.'php_action'.DIRECTORY_SEPARATOR.'temp'.DIRECTORY_SEPARATOR;
  //ofcourse we need rights to create temp dir
  if (!file_exists($PNG_TEMP_DIR))
      mkdir($PNG_TEMP_DIR);

  $filename = $PNG_TEMP_DIR.'test.png';
  if(isset($_GET['Descargar'])) {
    descargar($filename);
  }
?>

and in your form that contains the call of the Download button, change the action to this new file. Something like:

  <form method="get" action="downloadQr.php">

 <button class="btn btn-default button3" data-toggle="submit" 
name="Descargar" data-target = "Descarga"><i class="glyphicon glyphicon- 
  download-alt"></i> Descargar Qr en su Computadora </button>
</form>

With this, when you press the Download button, the download action of the file is called in downloadQr.php. It will send the headers that you define in the function, and it will download the file.

Manage the download call at the beginning of your file: Change the management of creating the file, towards the beginning of your code. Put the first thing of all this:

<?php
  include "includes/functions.php";
  $PNG_TEMP_DIR = dirname(__FILE__).DIRECTORY_SEPARATOR.'php_action'.DIRECTORY_SEPARATOR.'temp'.DIRECTORY_SEPARATOR;
  //ofcourse we need rights to create temp dir
  if (!file_exists($PNG_TEMP_DIR))
      mkdir($PNG_TEMP_DIR);

  $filename = $PNG_TEMP_DIR.'test.png';
  if(isset($_GET['Descargar'])) {
    descargar($filename);
  } else {
 ?>

Please note that I have set a else , this is so you can see first if it is defined to download and ONLY make the download (sending the file headers). This else must be closed at the end of your file, so that, if you have not asked to download the QR, it will show you the rest of your action.

MY RECOMMENDATION:

This whole problem comes up because you mix html and php process, and it is not very clear (and it is difficult) to organize these things. I would recommend that you start using MVC, review or use some framework (type symfony, codeigniter, laravel) to see how the processes are organized in controllers and views.