I absolutely HATE the collecting quests. Invariably, I will end up fighting at least twice the amount of monsters than the regular "fight X monsters" quests in order to complete it.
Just recently, while in DS, I did the side quest in the Crucible where you have to fight the minotaurs in order to collect mana sparks. I ended up having 19 battles (that is a minimum of 38 minotaurs, more since others had joined some of my fights) before I was able to get the 5 or 6 mana sparks.
Quite frankly, if someone gives me a quests to collect a certain number of items, and tells me that such-and-such monster has them, then I should have a better-than-50% chance of getting it from each monster that I defeat.
Oh, I can understand it when the item I'm trying to collect is a single item (such as the sword of mowagawa). That becomes more of a find the correct monster that has it, rather than defeat any of them in order to get. But the whole "Did not collect ...." thing has gotten way out of hand.
All you can do is keep fighting. Perhaps switch to a more crowded realm and try to find others to battle with. The more enemies in the circle, the greater your chances of getting at least one sample.