Just out of curiousity, are you actually clearing the dungeons on "normal"? Are you sure that you are not currently running on hard or above? It does indeed look like you have 1 of each item on the screen but if you get them on hard, they don't count. I know it's dumb and I've run into mission issues like this in the past. There are some missions that say "hard or above" or "3+* or above" but then there are some that are VERY specific in how to clear it. Wording it seems is very important on how you clear them.

I hope that I have the right solution for you.

Sadly, I am 100% sure I ran the whole thing on Normal enough times to get more than 1 of each piece :/

I'd likely contact support if I were in your shoes. Generally speaking these do end up being misunderstandings of some sort but support should be able to help you clear things up.