Regarding the "reward already received": the weekly restrictions on loot drops and the coins have been removed, but the restriction on materia clusters is still there. That's why you'll continue to see that message. You can see this in the duty description here:

https://na.finalfantasyxiv.com/lodes...y/f1a29897772/

As for particular non-gear drops, like the minions, they have always been random and do not drop in every duty. The only change in this patch is that you will only have to compete with people in your eight-person party to get them if they DO drop, not everyone in the raid. The intention was never to have them become 100% drops, and this was the case with the other Nier raids as well.