Summary:

This bug appears when the game process inventory changes from 2 sources simultaneously.

Steps to Reproduce:

1. Place the input and output containers and a hopper connecting them. Add a hopper locking mechanism (optional); 
2. Get multiple stacks of the same items (for example, 9);
3. Place a few stacks (2-3) of items in the hopper or input container;
4. While items move into the output, move the rest of the stacks into the output chest (with shift+click) as fast as possible;
5. Retrieve full stacks into your inventory and move them back into the container repeatedly until all the items from the input reach the output.

Observed Results:
Most of the time, you get fewer items than you started with.

Expected Results:
You should have the exact number of items in the output as you started with.

Notes:

• I’ve encountered this bug multiple times in normal gameplay when using super smelters, rearranging storage, trying to fill shulker boxes faster, moving items by hand along with hopper(s) going in;
• This bug seems to affect multiplayer more often and/or severely (probably due to latency/client-server lag);
• I’ve been able to reproduce it consistently only in the situation described above. Still, I suspect it can affect other similar conditions where items go into the same inventory or container from 2 sources, just less often;
• It does NOT affect when 2 hoppers go into the same container. Only if items going from the hopper(s) coincide with the player pushing items in the container simultaneously;
• The type of output container doesn’t matter. It affects chests, shulker boxes, and hoppers.

Attachments:

1-st video shows the above experiment performed in the creative single-player test world. Out of 9 stacks, 1 stack and 54 items were lost.

The second video shows the same experiment performed on a survival multiplayer server. I lost 3 stacks and 61 items out of 9 stacks.