I wonder if it's a bug in that feature. I tried it once when it first came out, but I have a few hacked Core files that I need to upload manually anyway so I just download - unzip - edit - delete old - upload new.
I don't think there's an easy way to determine if the auto upgrade feature has left other files. You could use your FTP client to look at file dates, but that would be time consuming and I imagine many files are repackaged unchanged from earlier versions and would be OK.
I've already upgraded to 3.0.1 but next version release I'll try the auto, download the files to localhost, then uninstall - install manually, download the files again and compare.
Until then I guess you have 2 choices. Replace only the wp-includes/deprecated.php file and hope for the best. Or install everything manually.
Seems to me if the auto feature was buggy the issue would have come up sooner, but who knows.