What you are describing doesn't make sense, so I assume I'm missing something.
If the payroll service only pays the net payroll, then where would it get the money with which to pay the taxes, unless it shorts the employees on their wages/salary.
If you mean that the payroll service used your business account to pay the taxes, even though you did not authorize the payroll service to do so, then my answer goes back to the original -- which is that the agreement you made is probably unenforceable. Once the payroll service is authorized to make payroll payments, it also has the obligation to withhold and remit payroll taxes
. It cannot simply pay over net payroll to the employees, without risking liability for the TFRP. The payroll service must
remit the payroll taxes.
Maybe you and the payroll service misunderstood each other -- or maybe the payroll service agreed to your proposed operational rules
, but then thought better of it and paid the taxes, because it realized that it was about to take an unreasonable risk.
I can't be sure of the rationale behind the payment. All I can be sure of is that the payroll service must pay the taxes or risk liability for them not being paid. If I were managing a payroll service, there is no way I would agree to pay only net payroll to employees.
Hope this helps.