I just installed the Custom Permalinks plugin today too, and like you I see the PHP warnings. Technically, those are "Notices", which is not an error. I'm not sure exactly what is causing the notice (could be an array which is look for a value in a key/value pair that does not exist...), but either way the notice won't hurt anything.
Actually, what you can do in your
wp-config.php file is to set WP_DEBUG to 'false') which you should not have set to 'true' for any site in production anyway) and the notices will no longer be displayed in the admin.
Alternatively, if you want to leave WP_DEBUG set to 'true' for a development environment, you can set WP_DEBUG_DISPLAY to 'false' in the file
default-constants.php (as long as you have recently updated WP, otherwise this may still be located in
Hope that helps.