You guys used masterloot?
We had this issue before, we now use round robin (need/greed) and have everyone turn off auto loot. Then raid leader and him only click on the corpse/chest to open it and click on the loot one by one for us to roll need/greed. we get 2 rakata pieces per nightmare boss, schematics, crafting mats etc.. no loot are missing.
It works well for when you have two identical items as well since you can have one person roll need on one of them and then the next person roll need on the other item.