Warnings On Updating WordPress

The issue is that the files cannot be written to by the web/php process due to permissions.

This is:

• Good! Those files can’t be updated with malware and other nasty surprises
• Bad! The updater cant update them either

So, I’d advise you do the following:

• Follow these chmod settings religiously What is true chmod for WordPress?
• Never use the auto-updater again. Instead use a more foolproof method such as an svn/git command, or downloading WordPress and uploading the new copy via FTP

This gives you a foolproof method of updating WP Core, without setting the write permissions in such a way that it compromises your security for the sake of convenience.

Given the warnings, I’d recommend doing the procedure again via FTP, clearly those files may not be the v3.5 files but older ones that it couldn’t write to.