Summary:
If you pick Health, Damage or Primary stat shard of the same type (For example base damage) to one was picked previously it won't work. I've confirmed this with Health, Damage and Primary stat shards on Sniper.

Repro:
1) Collect shards upgrades in Labyrinth until you get Health, Damage or Primary shard. I've tested this with Sniper.
2) Choose shard of the same type to the ones you already own.

Result:
New shard won't work.

Expected:
Bonus from both shards should work.