Please elaborate more on the circumstances and provide a test case (a simple 1, 2, 3 step explanation, including the used items), right not there's very little to go on - which means the following part could be totally off topic.
If I had to make an elaborated guess I'd say that the game does support adding items while a player is live but doesn't like it when the item count suddenly drops, the client caches some of these things locally and discrepancies between the server-side and the client might throw some parts of the game off course.
In case you need to do maintenance on the item stock, set the server to maintenance, log-out all players and do the changes. That should definitely get rid of the problem - and it's the way the official servers work as well.