I add files to the VLC app via both iTunes and via WiFi server. Via both routes, the video files appear as duplicates in the All Files menu. There is only one copy of each file, but it shows up in the menu 2-3 times or more. Deleting one copy deletes all copies in the list. Sometimes the image previews are different, but often they're the same.
This is running on iOS 8.1 and 8.2, iOS app version 2.4.1(1)