I was able to reproduce this multiple times, sadly losing a crate full of loot each time.
The key is to have 52 open slots in a field backpack, a shovel on your shoulder, and a wooden crate in your hands, and all clothing items filled to capacity.
If you rapidly press the SQUARE button, the cursor will move from your hands to your shoulder and the shoulder item will be placed in your backpack first because there is a delay and sound effect for the hands-to-inventory action. Since there was enough space when the first button was pressed, the game validates the request and proceeds to put the wooden crate in your inventory. However, because the shovel got there first, and there is nowhere else to put the crate, the crate and all its contents disappear.