Causes:

1. Invalid file type uploaded by the user your uploading (.doc when only .xls is allowed)
2. The file uploaded is not within the specified file types added in the upload config
3. Mime type error in codeigniter caused by the mime type of the extension does not match the mime type specified in /application/config/mimes.php

Start by checking what is the mime type of the file your uploading

$data = array('upload_data' => $this->upload->data());
$mimetype= $data['upload_data']['file_type'];
echo $mimetype;

then check in the mimes.php if that mime type matches the extension you want to upload

Example:
word document

'doc'	=>	'application/msword'

excel file has many mime types, if its missing just add it in the array

'xls'	=>	array('application/excel', 'application/vnd.ms-excel','application/x-msexcel')

In dealing with files on ci use the file helper
http://codeigniter.com/user_guide/helpers/file_helper.html

It is loaded using this line
$this->load->helper(‘file’);

read a file with read_file()
$data = read_file(‘./path/to/file.php’);

write a file with write_file();
write_file(‘./path/to/file.php’, $data, ‘w+’);

CI recommends “r+” but its better to use “w+”