Some items are simply more rare than the others.
For example vubbe fighter blood for crystal mine 3f collection is really rare and drops from a mob that is also not the most common in there. (Vubbe Fighter, the large-type monster that spawns on 3f)
Those that you are missing, I’m actually thinking they might be bugged OR are also quite rare. But considering that they’re just a drop from a regular mob makes me think that the drop rate is a little bugged on those two. I tried to do it this morning too, gave up after killing a bunch. I’ll just buy it later on the AH.
Bonuses stack.