It's the latter -- your stockpile on each continent is what matters, and you don't have enough materials of the specific type to learn those spells. If you hadn't unlocked the material yet, you wouldn't see the spell at all in the first place. Unlockables are not by continent anyhow (they are global to the world).
When it comes to how to find various materials, you'll want to use the reference info. Clay and such are not rare commodities, so you'll never get them from missions -- just break any vase you find inside buildings to get them. It mentions this in the reference info, so you know where to search. For raw amber, I'm not sure what you're referring to. If you mean yellow citrine, that's also not from missions. If you mean charred amber, that's a rare commodity mission but apparently it just hasn't rolled any of those for you in the randomizer. The secret missions will help you round out stuff like that when the randomizer doesn't do what you want.
