Low-level gems (like Ta Ondra Tara or Pyrite) that are used for low-level crafting recipes are incredibly rare (which doesn't make sense considering their low cost of like 80cp). After scouring about 70% of the map and thoroughly ransacking every dungeon, I have found less than 10 total. Some merchants occasionally sell one or two, but that's not nearly enough for regular crafting and enchanting. Similarly, I have found only a single Amber. Is this intended?
Unlike the original Pillars of Eternity, Deadfire doesn't feature an option to automatically procure crafting materials over time. To compensate, merchants and alchemists in the Deadfire should stock larger numbers and variety of crafting ingredients in general.