Upgrade to 3.0 can’t overwrite the php script that is executing the upgrade

I tried to do an automatic upgrade from WordPres 2.9.2 to WordPress 3.0 and I got this error:

PHP Warning: copy(<path to my site>/wp-admin/includes/update-core.php) [function.copy]: failed to open stream: Permission denied in <path to my site>\wp-admin\includes\class-wp-filesystem-direct.php on line 205

To me it seems that the file it’s trying to upgrade is the same file that is currently executing (/wp-admin/includes/update-core.php).

Although this is perfectly logical, it seems hard to believe that the WordPress programmers have not anticipated this. Shouldn’t this scenario be handled by WordPress. I can imagine that this affects exactly 100% of WordPress installs, or does it depend on the server configuration?