If you save before running the crosshairs over a malachite vein, you can reload until you get at least one gem. Two are not terribly hard to get and three are can be found if you are patient or lucky; four are rare, but possible.
For what it's worth, I only used malachite gems for healing auras (the rest I stuck to level 9 auras, as they have almost the same effect, but only require relatively common ingredients), so could have easily gotten by just with gems that could be purchased or had from quests.
