Stock quantity issues

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I am recently quite often experiencing situations where Shopify shows thre is stock on hand, while the item is actually sold out and should be 0.

These are not products that are marked to continue selling when out of stock and the original quantities when stock arrived were entered correctly. It is quite embarrassing when a customer orders such an item and they have to be informed the item is sold out. Definitley negative customer experiences.

I run another software programmme concurrently because Shopify does not provide me with financial management information reports I need to manage my business. That means when someone placed an order and I am executing the order, I record the sales on te other software (in the same manner that I enter stock purchases, prices, etc.). On the other system the stock levels are indicated correctly, so I am wondering of Shopify is correctly deducting sales from stock on hand?