(We've covered this issue in the past, but long enough ago that we've started receiving "new" reports of it from readers.)
MacFixIt Reader Gabriel Dorado describes a known bug in Mac OS X -- present since at least as far back as Mac OS X 10.2 -- where it is far too easy to delete the wrong folder when using column view in the Finder:
"Select column view, click a folder, create a folder inside it (Command Shift N), and immediately press Command Delete (or choose File -> Move To Trash) to delete the folder just created. Shockingly, the [enclosing] folder is trashed [rather than the new folder]! Worst of all, you may not notice such an effect because [the enclosing] folder may be hidden in the left side of the column view (particularly if you do not have it extended to take all the screen width). [The enclosing folder] may be your documents folder with all your files. If later you empty the trash, you may lose precious data for ever."
We've criticized this behavior a number of times over the past couple years. The problem is that when you create a new folder in column view, the new folder's name appears to be highlighted -- which it is, in an editing sense -- but the folder that is actually selected is the enclosing folder. We can see no logical reason for this behavior, as the expected (and, to us, logical) behavior is for the new folder to be selected. (And, in fact, that is exactly what happens in list and icon views.)
We hope Apple fixes this bug soon. In the meantime, users should continue be careful which folder they delete when using column view. (If you accidentally delete the wrong folder, immediately pressing Command Z or choosing Edit -> Undo Move of "foldername" will restore the folder to its original location.)