I can understand your concern. For them to get one code wrong might be regarded as a misfortune; to get two wrong looks like carelessness. It's often because there is some information or return missing - say a P45 from the previous employer. Give them a ring on the agent priority line with your client assertions. At the least it may bring to light further information or course of action.
Under RTI, HMRC have set up duplicate files for employees (especially if there has been a change in personal details during the tax year) and apply a BR code to the second file. When they receive the RTI submission they would apply the information to both files literally double counting that employee.
