I discovered the very same bug (MS probably calls it a feature). I have
the Documents folder shared on my work desktop and whenever I connect my
laptop to the network, Offline Files should sync with this share.
However, it seems that files created in sub-folders of the share are not
accessible, cannot be opened nor synced. Good going Microsoft!
Anyway, this happens because the sub-folders/files are probably
inheriting not from the shared folder but one of its parents. Open the
permissions prop sheet of the share and replace all inheritable
permissions of its children.