Server Got Hacked

[eluser]mrmeyers99[/eluser]
I've worked with a few websites with CodeIgniter, and in the past month (on different servers) two websites have gotten hacked. It's really weird, because the only thing that happens is the index.php file gets replaced with garbage (mostly links to drug websites and such). Nothing else happened either time. No database corruption. No other files were modified. The permission on the index.php file is 644. The host couldn't figure out what happened. Is there some security leak in CodeIgniter that would cause this to happen? What can I do to prevent this from happening again?