The New Commencement rule....!!

Hello everyone...The Finance act recently abolished the old commencement rule. But I recently encountered an organization that wrongly computed Tax computations based on the old commencement rule. The FIRS then raised up additional assessment based on the old commencement rule for the said organization to pay. Should this be allowed to stand?  Based on the fact the new Finance Act overrides the old rule? 

Since the old act is no more in force, it shouldn't be used to assess any company even if the period is later than 2019. The company won't be able to claim the overlapping tax paid at cessation.