Penalty for late federal withholding payment

Quickbooks suspended our money transfer license with no warning. We found out when we tried to send the first June pay period payroll data. So, we had to issue paper paychecks to employees and could not schedule on-time money transfers for state and federal taxes. Despite assurances from Intuit representatives that we would get it up and running, we found out that the MTL had not been restored. So, we spent hours on the phone talking with representatives, trying to fix information about the primary principal and master admin. We were told, two years ago, that this had been corrected. When the MTL was finally reinstated, we sent the payroll data to schedule withholding payments. Today, we got a letter from the IRS telling us that we had to pay a four-figure penalty. Intuit dropped the ball, prevented us from paying in a timely fashion and misled us, telling us that we wouldn't have to pay a penalty. All because they pulled our MTL without warning and mishandled the fix, jeopardizing our ability to pay our employees. I would like to know if we can appeal this penalty. If we cannot, I would like to know what Intuit will do to make us whole.