In the event that your inventory count comes out wrong. You may want to check the following.
When was track inventory enabled? If inventory tracking is EVER disabled, it will reset the inventory count. You can also disable the “Manage Inventory” permission to prevent your users from accidentally disabling inventory tracking if desired.
If sales have not synced, it could be a temporary discrepancy. Check receipts, are your sales syncing? If they are not syncing this can cause your counts to be off until the next count can be made. Sales can also sync late if the POS wasn’t connected to the internet. If you do an inventory count while the POS didn’t sync, it can throw the count off.
Are all your stock receipts and inventory counts booked? If not, this can affect the end count. It is a good idea to make sure your stock receipts and inventory counts are booked before starting a new count.
Is your warehouse for the product in a different org unit than your POS? It is possible that the POS Terminal could be assigned to a warehouse that is different from the organizational unit. This can be changed at the Point of Sale screen inside the Sales tab in the back office. This can be caused by the how the Organizational Units and Terminals were set up at the beginning of inventory tracking.