Two ways to get phials: crafting, and looting chests.
However, the phials gained in different ways cannot stack together. The ones crafted can only stack with the crafted ones, and so do the looted ones. To be more specific, when trying to stack them up, they appears to be stacked up into one stack, but once clicking the stack, it will immediately split into two stacks.
The problem seems to be caused by a fact that crafted Phials have tag/memory:none, while the looted ones don't have this tag.