I tested this with two tiers of alchemical essences, and there is definitely a bug:
I made a stack of 50 lesser cold (tier 1) shuriken, followed by a stack of 50 greater acid (tier 3) shuriken.
I initially dragged the lesser cold one to my inventory, followed by the greater acid ones.
What I ended up with was a stack of 99 lesser cold ones and a "stack" of 1 greater acid shuriken.