The green 'malachite' is malachite ore, which is easy to get; the red is a malachite gem, which is much rarer. I have no idea why the PC version abbreviates both to just 'malachite'.
In D2:ED I got 28 total in the game; I don't think you can get as many from malachite veins in DKS, but there are more from quests or merchants in the FoV section. In D2:ED, by saving before running your crosshairs over a malachite vein you could reload to make sure you got a gem; 1 or 2 were relatively easy to get, 3 could be gotten with patience or luck, and 4 were possible but very rare. In DKS at least other gems seem to be more limited from veins.
In D2:ED malachite gems were required for any level healing aura (still the case in DKS), and 3/4 of the other level 10 enchantment auras (don't have any yet to check).
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