Update 19/04/17: If you are using G Suite Business or Enterprise you should be using Team Drives to share files to avoid orphaned files.
Google Drive is fantastic at storing all your documents and sharing them out with colleagues. But, due to the ease of sharing you can sometimes find yourself with orphaned files.
Files get orphaned in Google Drive due to conflicts with folder sharing and permissions.
User A creates folder X in his Drive.
User A shares folder X with user B.
User B creates item Y inside folder X.
User A trashes folder X, and empties his trash.
At this point, item Y becomes orphaned. It was never created inside of user B's My Drive, and its parent folder (folder X) is now gone. Note that item Y is not deleted along with with folder X because user A can't delete user B's file.
To better understand how an orphaned file or folder can come about watch this video. And remember the rule: Never remove a file or folder from inside a shared folder!
To find an orphaned item, do one of the following:
Search for the item in the search box at the top of Google Drive on the web. Using the search query is:unorganized owner:me
If you own the orphaned item, you can get a list of everything you own and look for the item in that list. Click the down arrow in the Google Drive search box and select Ownership > Owned by me
If you've accessed the file recently, click Recent in the left navigation and then browse for the file.
Once you find the orphaned file, you should move it into My Drive (or another folder), to give it a home and make it easier to find in the future.