The link @Lubos provided all the “factors” that affect quantity on hand in the section “…Accurately Reflecting Physical Inventory…” but let me simplify this:
To ensure an accurate quantity on hand in Manager you can only use:
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Delivery Notes and these MUST be linked to Sales orders (not quotes or invoices!), and
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Goods Receipts and these MUST be related to Purchase orders (not quotes or invoices!)
“Qty on Hand” then shows the actual inventory movements - receipts and deliveries of the items - and not just invoiced transactions.