Items with unsupported data values stack on certain events such as item pickup and shift-click

For instance, say I give myself one emerald and place it in a chest.
/give VergilPrime 388 1
then I give myself another emerald with an ID of 1
/give VergilPrime 388 1 1
If I shift click the 388:1 into the chest, or the 388 into my inventory, they will become either a stack of two 388 or a stack of 2 388:1.
If have both in my inventory and throw one on the ground, then pick it back up, it will stack with the other and lose its data as well.