When an item in the player's inventory has nowhere to go with shift-click, shift-clicking causes it to disappear. This includes the excess items from shift-clicking stacks into containers.

Example 1
Shift-clicking 64 cobblestone into a furnace that already has 63 cobblestone will cause 63 of the shift-clicked stack to disappear permanently.

Example 2
When the player's hotbar is full and there are no doors in the player's hotbar, shift-clicking a door in the player's inventory when no containers are open will cause the shift-clicked door to disappear.