I had no idea that all media from the media manager is bundled with an app, even if the media is not used in the current app. This is a major pain in the rear, not least because the media manager does not include bulk delete, so it has to be done file by file.
This should definitely be changed so that only media used by the app is bundled, or an option is included in the App Settings to opt in/out of bundling all media manager files.