There was the kerfuffle at the start of the month with QuickPick. Apple rejected an _update_ to an app that was already on the Store that duplicated (future) built-in functionality: http://www.tuaw.com/2011/04/08/quickpick-update-in-limbo-for...

The original version of the app is still up on the Store, but the update was rejected. Which is confusing.

They did during the Google Voice fiasco. A bunch of third party GV apps that were already approved (GV Mobile was one [1]) were pulled. Since rectified, but has happened before.

1: http://www.seankovacs.com/index.php/2009/07/gv-mobile-is-get...