Yea not sure why everyone in the walkthroughs is saying save them or use them wisely.
There are plenty of them around.
Just earlier I got 5 of them out of the tomb with the grave robbers quest.
3 out of the vein on the right and 2 out of the vein on the left.
I'm carrying around 13 right now and not sure how many I have in my battle tower chest.
Think I only used one or to for enchantments so far.
The enchantments the Malachite gems are used for are not very good or useful ones the way I see it.