When trying to upgrade 2.7.0->2.7.1 I get
Downloading update from http://wordpress.org/wordpress-2.7.1.zip
Unpacking the core update
Could not copy file: /wordpress/wp-content/upgrade/core/wordpress/wp-trackback.php
The problem seems to be that the files are uploaded as the ftp user which is different to the apache user. The file permissions are set as 711.
I thought I has cracked it by setting the FTP server umask to 113:002 (apache and the ftp user are in the same group), but while this seems to correct any permissions on file I upload myself, the files uploaded/unpacked during the upgrade process still have permissions of 711.
Unfortunately manually setting the permissions on files that are complained about (as suggested by pal0216) doesn't work because the files are re-uploaded (and so permissions reset) each time I restart the upgrade process.
Something in the upgrade process to chmod the files (using FTP) as required would probably fix it.
Sorry it doesn't solve this, but hopefully it adds some more insight into the problem.