warped quarry
This upgrade dialog is stuck, because I don't have enough minerals in each stack (soul linked and normal), but when adding those together, it would be enough minerals, so the upgrade dialog rightfully allows me to progress. It's just, the logic seems not to work when resources are spread on several stacks when they only are enough when combined.
timber nova
Had this happen aswell. Instead of using the items, they Just swap places in the inventory. As an easy fix, you can Soul Link the correct amount of regular Mats, so they add Up to the necessary 75 total
rose sonnet
You need to make sure your character is near in the npc. Sometimes position bug happens. Atleast you need to jump multiple times to fixed position and to make sure that your character is near to the npc.
warped quarry
You need to make sure your character is near in the npc. Sometimes position bug ...
sorry, this is not the case here. I converted both stacks to be soul-linked and the issue resolved itself immediately.