With dept level inventory there are only a few things really to check.
Purchases:
1. Are any missing?
2. Are the margins correct on each purchase?
Check this report: reports->nonfuel inventory->non fuel invoices by vendor
Mark ups/downs
1. Are the markups and mark downs being put in via non fuel invoices?
2. The mark up/down non fuel invoices should be using 'inventory adjustment' as the vendor. You can run the same non fuel invoices report to see these invoices. Every retail change in the system should have a corresponding mark up or mark down invoice so dept level inventory can make the adjustment.
Default Margins
1. Please check to make sure default margins are set correctly. Incorrect default margins can lead to wrong cost being figured,etc... So it's important these are correct.
Check margins via the following window: Inventory->maintenance tools->define c store profit ratio
There is no smoking gun with this....it's just knowing what to look for and research. We don't know what goes on at the store to be able to see what is right & wrong, but I can give you some tips on how to research.