Question: Non deductible expenses in Company Return.

The system is picking up the wrong super amount from the balance sheet in non-deductible expenses

Answer:  The Superannuation showing in the reconciliation is a payable and not an expense because (paid after 30 June). Since entry for this is 

Dr-Superannuation Expense and

Cr-Superannuation Payable 

There must be an expense showing in the Profit &Loss section.

Related guide: Unpaid Superannuation in the Reconciliation

Amount under the Non-Deductible part of the "Reconciliation", this is the amount of Superannuation Payable in your balance sheet for the current year.

Logic behind this is that this liability is usually paid the following year.

ie the $3,631 amount under "Other Deductible Expenses", this is the Superannuation Payable in your balance sheet in previous year.

This liability is expected to be paid on your current year of your tax form being prepared.

Reference guides: Accrued Superannuation (Unpaid Superannuation)

Please note that the reconciliation section purpose it for your Total Profit/Net Profit per accounting books to arrive with the Taxable Income which is the basis of the tax rate. 

The financial information section serves for a other purpose with regards to computation of your tax payable/tax refund.

 This is the reason why the Superannuation Payable is added or deducted base on the tax period it was paid and not on the year it is recorded only. Learn more here -Logic of Reconciliation Section. 

If you want the Superannuation Payable to not reflect in your tax return, then go to Financials > Accounts

Click Liabilities tab, then

Scroll and find the "Superannuation Payable and change the tag to "Do not import to tax return"

In this case, you need to manually add it the tax form as you see fit (see yellow highlight box below).