I used to see the single missing folder issue where the user had inadvertently dragged a folder of e-mails into another folder (or sometimes a folder of files on the fileshare).
Ooh, that reminds me of the time one of our developers put a textbook down on top of his mouse, whilst the files in Visual Source Safe were open in an Explorer window which had focus, and managed to drag and drop half the projects into an unrelated folder. Cue panic as he looks at the screen to find all his source code suddenly missing...