The GST amount captured in the BAS is coming from all transactions coded with the tax code. We'd recommend running a Transactions by Tax Code report and your BAS Detailed report and compare the figures if they match.
To run the Transactions by Tax Code report:
Click on the GST tab, and click on Run Reports.
Click on Transactions by Tax Code report.
Select a report period and accounting method, and then click on Run Report.
Look for any transactions which may have been coded with GST code incorrectly and edit the transaction.