it is not intended that you always get doubles but here is how the second layer crystals work

it scan's you're list of t2 crystals for a crystal you don't have, how many crystals it goes through and how it scans them i dont' know, its prob some random crytsal selector

if it doesn't find one you need, it will try again, up to 3 times

if it still does not find one you need, it will give you one that you already have

so best bet for minimum duplicates is to add them to your collection BEFORE you complete the T1 shard set again

but it comes down to statisics, the more crystal's you have, the less likely it will be for it to find one that you need because of its random selection nature