How to reproduce:
Create a custom item, with a custom "maximum stack limit" (ex: 16)
Place multiple stacks of items in a chest
Shift click, or shift craft multiple stacks of items, such that the new amount is greater than that of a stack
Observed results: The excess is deleted
Expected results: The excess items are split into a new stack, leaving the previous stack at its maximum value
Unsure if this was fixed in the beta. I know that eating animations for custom food were fixed, so maybe this was too.