Not all media is ignored by iCloud Backup
There are ways to sneak media into the app without having them flagged as disabled for backup, notably using iTunes, because "updateMediaList" is not performed on the VLCMediaFileDiscoverer shared instance.
This is most likely caused by the 1f034b70 mega commit, which disabled the unconditional execution of this selector when the app moves to the foreground. In this monster code dump, it is not documented why this was disabled.
see also: https://forum.videolan.org/viewtopic.php?f=36&t=151430