The June BAS is wrong the PAYG Withholding figures are wrong, right on balance sheet and other reports wrong in the BAS area, were right last quarter no explanation

I want to make sure you're compliant with the ATO rules and regulations, @Annette-H. That's why I'm here to provide the steps to correct the differences in your BAS for June in QuickBooks Online (QBO).

Here are the possible factors why the PAYG Withholding figures are wrong, and the other reports display incorrect amounts in the BAS area: 

• The Accounting method for GST and reports is inappropriate. 
• The Report period in the reports and Lodging frequency in the tax settings doesn't match with each other. 
• You've made any changes to the filed transactions (Exceptions), which affects the BAS and PAYG balances for June. 

There are things we'll need to perform to help resolve your concern. First, let's go to the Tax Settings window from the GST menu to review your tax setup. Make sure to take note of the Accounting method and Lodging frequency for GST. Then, also check your Lodging frequency under Tax withheld for employees (PAYG Withholding). View the screenshot below for your reference. 

Second, let's pull up the GST Details report from the Reports menu. If your lodging frequency for GST and PAYG Withholding is Quarterly, I'd suggest choosing the Last Calendar Quarter as the Report period. For the accounting method, select your assigned Accounting method based in your tax settings. Then, choose the appropriate GST agency from there. Doing so will help you locate the differences of your BAS for June. The screenshot below serves as your visual guide. 

Third, let's run the GST Amendment and PAYG Withholding Amendment reports (see the screenshot below). From there, we can review if you've changed, deleted, or added transactions you have already filed. If you're able to view the exceptions from there, I'd suggest contacting our Customer Care Team. They can help you unlodge the previous BAS and provide you further assistance regarding it. This way, we can ensure that the amounts will be correct for the current filing period. If not, you can proceed with lodging on the BAS for June. 

Lastly, I recommend visiting this website: GST Central. This is a resource hub that'll help you effectively manage your GST centre, BAS filing flow, and Other taxes in QBO. 

Don't hesitate to leave a comment below if you need anything else. I'm always up for assistance, @Annette-H.