When you do a "Bulk Remove Deleted Videos from Playlists" we go through and remove Deleted videos from your selected Playlists.

Apparently there are videos that no longer exist or the channel was suspended because of 3rd party copyright claims and the data within YouTube's system is messed up. In those cases, we unfortunately can't delete the videos and you will need to go in and manually fix it. 

Here is an article describing some of the problems: http://stackoverflow.com/questions/43049934/removing-a-playlist-item-that-is-a-deleted-or-privated-video