A solution I found was when you're looking at the A/R report in QB, click on the "Customize Report" button at the top, then the "Filters" tab, then find the "Amount" filter and click on the circle that selects the >= option and type in 0.00 for the amount and this will filter out any negative balances. You could also use the and put it as 0.01 to filter out any zero balances. 

Hopefully this helps anyone.