Usually, users can track the transactions making up for the difference for both reports by creating a transaction saved search for the accounts composing the BAS (W1).
Users can follow below steps:
1. Navigate to Setup > Company > Business Activity Statement
2. Take note of all the accounts under Total salary, wages and other payments (W1)
3. On a new tab, navigate to Reports > Saved Searches > All Saved Searches > New
4. Choose Transactions.
5. On the criteria tab, add filters:
a. Account = add all the accounts listed on your W1
b. Date = within 1/6/2019 to 30/6/2019
6. Click Preview or Save&Run
7. On this report, users can verify the negative amounts that is causing the difference on both reports.