Dear Ranajoy,
Your question pertains to Supply Chain and Logistic Management, not HR. You have posted the query here, perhaps thinking that since HR people conduct job interviews, they can/should answer the query.
I have sufficient domain knowledge to recommend the following response to the interview question.
If the Logistics/Supply Chain manager is maintaining a Computerized Inventory Management system, then at any point in time, he will know the exact quantity of an item, as all receipts and issued materials are updated in real-time.
But if somebody tells you that some SKUs are missing, then without going to the warehouse and checking it physically, you can ascertain the position sitting from your chair by calling the storekeeper on the phone, telling him the item code, location or bin numbers, and the quantity in stock (taken from your system), and ask him to ascertain the existing quantity.
If there is a shortfall, it can be attributed to errors in issue or receipt, or pilferage/theft.
Issue a show-cause notice (SCN) to the storekeeper, in consultation with HR, while keeping your superiors informed.
Warm regards.