Ajax to display multiple error messages.

You don't need this part at all:

PHP Code:

if (!$json) { 


since $json will always be not true.

Also, you want to save error for every not uploaded file so correct nesting would be:

PHP Code:

if ( ! $this->upload->do_upload($fieldname))
{
    $json['error'][$i] = $this->upload->display_errors();//note that $json['error'] becomes array
    $check_if_any_error++;
} 


After that what is left is to save success message if all files are uploaded with no errors:

PHP Code:

if ((int)$check_if_any_error < 1)//or alternatively if (count($json['error']) < 1)
{
    $json['success'] = 'You have upload your selected files!';
} 


Then, handle response well as you get (if any) array for errors.