NeoArkadiaFrom Manga Entertainment:
According to Ravegrl, the issue is that 5D's episodes are included on the disk, instead of GX episodes.
Due to a manufacturing issue, Yu-Gi-Oh GX Season 1 has been recalled. You can return your copy for a full refund and fixed stock will be available in a few weeks’ time. We sincerely apologise for the frustration & inconvenience caused.
According to Ravegrl, the issue is that 5D's episodes are included on the disk, instead of GX episodes.