Yes, QB doesn't know you applied an over-payment on the form from Q2 to Q3. That information only exists on the form.
In this case, one option is to just ignore QB because you know you paid the tax. If you do that, the due amount will drop off in a year or so.
Or, you can enter two liability adjustments, one with an effective date in Q2 to artificially increase the balance due - matching the over-payment amount, and one for Q3 to reduce the liability by the same amount. Start at Employees | Payroll Taxes & Liabilities | Adjust Liabilities. Mark both transactions as "Do Not Affect Accounts" by clicking the Accounts Affected... button.
