Perhaps they physically moved (shipped) the inventory before they counted it. Once they freeze, they need to count inventory before they start shipping or receiving (that is before they start moving the inventory). Shipping prior to counting could create negative QOH now (they count less on the floor and then the system also reduces QOH by the shipping).
Or, perhaps they posted something to September after the freeze and the system is doing what it's supposed to do, just that you/management didn't know about that posting.