Automatic Plugin Upgrade Feature
Confirmed (2.5 RC1)
- Several existing plugins, in particular database-tied plugins, require a deactivation prior to upgrading, the automated mechanism doesn't do that
- Some plugins require specific actions taken in your theme files or even WP files to work, the auto updater cannot do it
- Some plugins are currently not yet placed in a proper directory structure which is compatible with the autoupdater.
http://www.blogherald.com/2008/03/18/wo ... -problems/
If you bork your installation with a plugin and don't know how to debug it, simply rename the plugin folder through FTP, it will get deactivated that way.