Duplicate transactions are usually generated when the order in question is left open across multiple reporting days. i.e. order is created on Monday at 5 PM but not closed until Tuesday at 8 AM. The reporting period in question starts at 3 AM. This will generate the alert on the Sales Summary page that says 'This order period has some orders that may be duplicated in other reporting periods.' Easy way to verify this is to open an order in question and check its open/close status at the bottom.
Duplicate orders being reported at the top of the Sales Summary