I am not completely sure about this, but I would expect that behaviour to be determined by whether the item in question can be considered 'generic' or 'unique' in some sense. If the item is 'generic', it will be deleted, and an inventory counter incremented for the container.
You could try attaching a script to the object in question to make it a 'unique' instance. Depending on the specifics of your situation, there may be other ways to achieve 'uniqueness' (like being a quest item), but perhaps someone else knows more about those.