Based on 1.11.2 decompiled using MCP 9.35 rc1

The bug

Shift clicking an item stack with a count greater than 1 and slots which allow this item but have stacking restrictions can result in multiple slots being filled.

Code analysis

Based on 1.11.2 decompiled using MCP 9.35 rc1

The method net.minecraft.inventory.Container.mergeItemStack(ItemStack, int, int, boolean) does not stop distributing the items of an item stack once it successfully placed some of them in a slot.