When WordPress checks for updates it runs a check for theme and plugin names against the WordPress.org directory to check for newer versions. So, in the case of themes it checks the slug of the theme as well as the title of the theme. If it finds a match, it prompts the user to update.
That’s exactly what happened in Cristian Antohe’s case, except that his theme was never added to the WordPress.org theme directory, and his users unknowingly upgraded themselves to a different WordPress theme.
Antohe had created a theme called Commune, a child theme of the popular WordPress theme framework Thematic. He chose to never upload it to the WordPress.org theme directory, distributing it via other means. Then, recently, another theme author created and uploaded a different theme to the directory, also called Commune. Since the slugs and the theme titles matched, this queued up the theme for an automatic upgrade for its users.
This sort of thing has come up once or twice before, though Antohe has explained his situation well with his blog post, and linked to a relevant ticket on Trac (since closed as a duplicate of this one) and a tutorial by Mark Jaquith for removing themes and plugins from the automatic upgrade check.
This problem isn’t a common one, but could be something you’ve run into before. Have you ever had a theme or plugin update itself to something you didn’t intend? Have you used any specific techniques to avoid this problem from occurring with your own work?