Except that's not how it works at all, the breaking of parts adds individual rolls for the boss's units yes and that is most likely applying to the red crystal too, since that one is just a condensed version of all the drops you have collected over the course of the UQ, the amount mostly depends on how much stuff you actually kill.
In this EQ there can be a high variance of what actually ends up spawing, you could run through the entire thing and only get the Chrome / Gemini combo at the end, that would result in almost no drops, while getting rare variants of bosses will significantly increase the amount of rares you will get.
Ultimately the amount doesn't really matter that much, except for Egg's this UQ doesn't have anything that's really worth getting aside from maybe the Souls and from what i've seen those are usually attached to Units that aren't in the boss's usual droptable so they might be zone drops from the crystal.
In the end we can't know for sure and i'm sitting here wondering what you felt like was stolen from you, except maybe a couple Ex-Cubes