This is not a bug.
The current version of NWN has the option of:
Destroy an item if it cannot cast any more spells, even if it has charges left (even if it has use per day left, if the use per day has been used today)
Don't destroy the item (unless it's a single use power, using that always destroys an item) even if it runs out of charges.
We chose number 2 because number 1 sucks.