Are you sure you had the extraction passives, have you double checked your crafting bag to see nothing was added.
I don't think you are unlucky I think it bugged. A hundred refines is too many not to receive any upgrade mats.
Maybe it's just been luck of the draw, but I've noticed in the past for myself diminishing returns when refining in bulk. So I only ever do a little bit at a time now (maybe 100 at the most at once), and that seems to work fine.
When I did bulk, after a while you'd get nothing back but the ore. Maybe just un-luck for me? Unsure, but I play it safe. Precautionary principle.