There might be amounts that are taken out of your Cash Drawer that weren't recorded. Make sure to record any bank deposits to make sure there are no discrepancies at the end of the day.
It's also important that when running the Count Drawer report, make sure that the Starting Amount is correct.
In addition, you might need to physically recount the number of bills and coin type when reconciling your cash drawer. This is to reduce the chance of shortages and error when entering the amount of cash on hand in the register.
Lastly, I would suggest reaching out to our phone support so they can help you review the shortage and help you make adjustments.