There seems to be a weird duplication bug, when taking out items the "wrong" way.

First take an item stack of something by left clicking. Here a stack of gold.

Press shift + left click on the remaining items.

You get a new stack of the item without draining from the warehouse each time you click shift+left click. Here the number of gold stays 427 in the warehouse while additional stacks of gold appear in your inventory.

Item duplication is really possible. I've found this bug muself.