AJAX Validation error on forms with file upload field + select with multiple options enabled

What are the steps required to reproduce the bug?

1. Create a form in code.
2. Add a select field with multiple selection enabled.
3. Add a file upload field.
4. Attach an AJAX callback to the select field that just returns the same form.
5. Choose more than 1 option in the select field. The system will show the following validation error: An illegal choice has been detected. Please contact the site administrator..

Here's a sample custom module that demonstrates the issue:

File: sample.info:

name = Sample module
description = Sample module for testing the validation callback of AJAX enabled select fields.
package = Custom
core = 7.x
version = 1.0

File: sample.module:

function sample_menu() {
  $items['sample'] = array(
    'title' => 'Sample form page',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('sample_page_form'),
    'access callback' => TRUE,
  );

  return $items;
}

function sample_page_form($form, &$form_state) {
  $form['#id'] = 'sample-page-form';

  $form['list'] = array(
    // This does not work.
    '#type' => 'select',
    // However if the type is changed to "checkboxes", validation works properly.
    // '#type' => 'checkboxes',
    '#title' => t('Select something'),
    '#options' => array(
      'option1' => t('Option 1'),
      'option2' => t('Option 2'),
      'option3' => t('Option 3'),
    ),
    '#multiple' => TRUE,
    '#ajax' => array(
      'method' => 'replaceWith',
      'wrapper' => $form['#id'],
      'callback' => 'sample_page_form_ajax',
    ),
  );
  $form['file_upload'] = array(
    '#type' => 'file',
    '#title' => t('Sample upload field'),
  );

  $form['actions'] = array('#type' => 'actions');
  $form['actions']['submit'] = array(
    '#type' => 'submit',
    '#value' => 'Submit the form',
  );

  return $form;
}

function sample_page_form_ajax($form, $form_state) {
  return $form;
}

What behavior were you expecting?

To be able to select multiple options in the select field with AJAX callback, without validation errors.

This works properly when using `checkboxes` instead of `select` form element.

What happened instead?

The system showed validation errors instead.

My investigation

I narrowed the problem down to the following: when a file upload field is added to a form, values submitted from a select field with multiple options enabled will be passed as comma separated values instead of arrays. This triggers the validation errors because the system cannot match the submitted value with the values defined in the #options property of the field.

Here's what I mean:

1. Values passed without the file upload field:

   Array
   (
     [list] => Array
       (
         [option1] => option1
         [option2] => option2
       )
   )
   

2. Values passed with the file upload field:

   Array
   (
     [list] => Array
       (
         [option1,option2] => option1,option2
       )
   )
   

Let me know if you need any additional information.

Thanks!