My payroll company paid my 940 and 941 payroll taxes for me for 6 months last year. They did this by mistake when they changed over to a new system.

I paid my taxes also. I have a payment plan in place with the iRS with a large balance. The payroll co. now wants me to give them the $12,000 back that they sent to the IRS. The IRS has or will apply it to my back taxes and refund any left over. My question is: Do I need to make arrangements to repay them, or is this a case of "their mistake my gain?" Can they come after me for the money? This is the biggest credit card processor and payroll company around.