Pretty simple, really. Make it so that materials can only be found in the clockworks, probably at an increased rate, and NOT in the mission mode. (unless it's a reward for said mission.).
My reasons for this are pretty straightforward:
1: We need an incentive to either A, go back to the clockworks, or B, to NOT do the mission mode.
2: It severely devalues your "rare" material reward in a mission when you can, yknow, find it in that same mission. At that point why even bother giving it to us? We're going to find it anyway.
3: Honestly, materials have devalued so much they're practically worthless, despite being completely necessary to craft any kind of equipment. This would be a great way to increase the demand for materials, and also the price.
I wholeheartedly agree. I assume crowns are able to be collected on these missions however, so it's not totally game-breaking.