If you shift click items into a chest/hopper/dispenser/furnace etc. that has items being pushed into or pulled out of it, the number of items you end up with can be lower than the number of items you start with.

Steps to replicate:

1. Have an inventory of items.
2. Create a series of chests and hoppers such that each chest is connected by one hopper.
3. Shift click the items into each of the chests and hoppers.
4. See that the number of items in the bottom chest at the end is not the same as the number of items you started with.

Expected outcome:
The number of items won't change.

Actual outcome:
The number of items is less after shift clicking items.

https://drive.google.com/file/d/1s9gJa2lUnzw5zYjptnyTROoQTsFFHXZz/view?usp=sharing

In this video, I started with 36 stacks of iron ingots. After shift clicking these at random between the top two chests and hoppers, I ended up with only 35 stacks of iron ingots.