I have this plugin installed under Yanfly's Item Core.
Here are some screenshots, to show what I mean:
Spoiler

The Wooden Sword isn't marked with "<Non Independent Item>".

The Torch, on the other hand, is.

The event where the warehouse is created. (The second page is just the "opened box" graphic with the "show <Box>" plugin command.)

These items work perfectly fine, thanks to being marked with the <Not Independent Item> tag. When these items are selected, they play the "select" sound effect and are removed from the warehouse. The "Available Space" section changes to reflect this.

It's these items that aren't cooperating. When selected, they play the "buzzer" sound effect, and do not get removed from the warehouse. The "Available Space" section also does not change.


As expected, the inventory shows one Pickaxe and one Torch. But it also shows two Wooden Bows and two Wooden Swords, as you can probably see from the notifications in the top right corner. From top to bottom, the notifications read:
Obtained Wooden Bow x1
Obtained Wooden Bow x1
Obtained Wooden Sword x1
Obtained Wooden Sword x1
Obtained Pickaxe x1
Obtained Torch x1
Hopefully this is either an easy fix or a case where I missed something.