My federal return balances out my provincial so that I owe nothing but in the review section on the "File now and pay your balance later" it says that I still owe money.

While you prepare the two returns together at the same time, you're still filing a distinct and separate return to each revenue agency. So, you need to pay your tax balance to the agency you owe to and wait for your cheque from the agency that owes you a refund.