Interesting observation. I have several J-Nats and several Naguras, from soft to extremely hard.
I have a questione: did you flatten your nagura?
I always flatten one sinde slightly, so there are no high spots that can easily scratch a stone.

Even my hardest nagura do not scratch my stones unless I use them incorrectly: too much pressure, or unflattened.

Donīt jump into conclusion about the hardness of your stone and nagura because of random scratches from your nagura.
This doesnīt necessarily mean your Nagura is harder than your Ozuku.
However one thing kinda startles me, why did you asked for a Tomo Nagura softer than your Ozuku?
Usually you specifically ask for the hardest Tomonagura. I donīt see a problem because it probably doesnīt matter that much, but Iīm curious