Guessitmate, that as VFF and ANA are in an agreement, but not a full *A alliance to alliance membership, VFF can be quite picky on what they will accept, ie, they might not accept the cheaper fares on NH.
There might also be no tie in for the fare class, that NH will sell on Japan dom fares, but for which VFF does not have the fare code on their system.
VFF might only have some of the 26 alpha codes, re fare class, NH might have more code designators.
Hard to say tho, as to why VFF would not accept that NH Japan dom flight class.