Drupal currently executes functions in include files. This is very annoying if you want to include files from external scripts such as update scripts or other scripts that want to use Drupal as a framework.
Offending files are:
session_set_save_handler("sess_open", "sess_close", "sess_read", "sess_write", "sess_destroy", "sess_gc");
A bunch of stuff at the bottom.
All this should be moved into a start.inc file.