Wages paid in advance and ATO Verification report

Hi, 

 My ATO verification report is out compared to my Payroll Activity and Payroll Register reports on desktop.

It is exactly the amount of wages that have been paid in advance.... 

As the "wages paid in advance" are adhoc and a short term loan... they are not reportable till the wages have been earned... As per normal payroll... then the repayment is processed as a deduction to settle it...

Am I missing something here?

Do I just proceed with the EOY finalisation as is?