Note: I only have experience with Online mode, so select that for the mode.
I am doing the quest line for the portal stabiliser and have twice accidentally used my pellucidic ingot to craft with / repair a structure. The first time, it was applied to an NPC's cooking station and I had to spend time crafting extra stations to finish the repair, and then destroyed the station to get the ingot back. The second time, it must have been used in a repair during an aid quest and I wasn't able to track down where it was used. I'll have to go back to re-acquire the quest item from the Sun Giant.
Suggestion:
Please allow us to "lock" items to prevent them from accidentally being used in crafting.
Secondary suggestion:
Please allow us to remove items from the repair / crafting window and replace with another item that's not a quest or fabled item.
As a bit of a middle ground, I think it could help if there was some sort of gold border around quest items. To highlight what it is used for an active quest, and alert for a person if they may be about to use a quest item or not.
I'm not in favour of this, I feel that you should just be more careful. It's not that I feel harshly toward you, or others that have experienced this. I just feel that at a certain point, people need to take responsibility for the things they do, even the things they do carelessly, and stop expecting the game developers to make features to hold their hand every step of the way.