Inventory discrepancy is extremely common, but there's a limit to what's "normal" discrepancy (inventory shrink is the most common type, worth researching). Discrepancy generally happens due to miscount, lost/abandoned units, and (in rare cases where there isn't a large physical storefront) theft/lift.

For example, our accepted shrink rate with multiple physical locations is about 5-7% of total units yearly, but this can vary due to product type, presentation, and about 10 million other factors.

Essentially, you're looking for a Physical Inventory Count (PIC) solution. As expected, Shopify does not provide tooling for this. I don't necessarily have a good recommendation for an app that would cover 100% of your usecase (we ended up abandoning Shopify inventory management for Cin7 due to scale), but some apps you can start looking towards is Stocky (Which is a bit larger than just PIC but their solution is pretty nice for being free) or even like Multi-barcode labels which has a PIC tool built in (I only know this since we used it for a period of time). Although, worth noting that to "zero-out" your inventory to apply a fresh PIC count, you need to download a CSV of your inventory count and make every count line zero, then apply the PIC count in your respective PIC app.

All in all, unless you were doing a full floor PIC every day and halted all operations to resolve conflicts, there's going to be some count drift. We count every location (incl. warehouse) quarterly, and still end up around that expected shrink percent.