As per GST Rules, the value of supplies include
(a) any taxes, duties, cesses, fees and charges levied under any statute, other than GST
(b) amount supplier is liable to pay but which has been incurred by the recipient.
(c) incidental expenses, such as, commission and packing, charged by the supplier
(d) interest or late fee or penalty for delayed payment
(e) subsidies directly linked to the price excluding subsidies provided by the Govt
As you can see point (a) which may include penalty due to guidlines violation.