The news this week of Such underpaying staff in their retail business going back to 2010 is a reminder of the importance of checking and cross checking payroll calculations and processes. Before the Lush story there were the reports abut the Rockpool payroll and entitlements issues and there in hospitality. Prior to that it was 7-Eleven.
My suggestion is that you get someone from outside the business who is not involved in managing your payroll or staff entitlement record keeping to do an audit of your calculations and your processes.
It would be better for you to find and resolve the issues than a regulator to force this on you as a result of a formal complaint.