The use of folders in zotero is unintuitive and goes against the accepted desktop metaphor. An item should not be in more than one folder at a time. Just as a book, or a video can not physically be in two places at the same time.

While it is useful to sort an item into multiple categories this is the same functionality that tagging offers!

Apart from the misuse of the folder metaphor the reason this is annoying is that there is no easy way to sort though a large number of items and see what has been left over.

If the items only appeared in one folder at a time then I could easily see which ones remained!