This is not something that I've experienced directly but I've answered it multiple times on the forums in the past couple of weeks. It seems that when a quest or a junction requires a specific item to be crafted to progress, if the item is claimed via the mobile app it won't count towards the quest in game. I'm not sure if starting the build via the app and claiming it in-game makes any difference (I'm all quests done until next update so I have no way to test this right now), but definitel