Analysis of the negative impact of a mechatronic system with the flexible elements parameter error and the possibilities of impact reduction are presented in this contribution. Two advanced methods – the Model Predictive Control method and the inclusion of an LMS filter into the control process are proposed for the reduction of the insufficient effect of a double notch filter, which was initially integrated into the system for elimination of two-mass flexible joint parasitic frequencies. Simulation experiments results – response of system angular velocity and control process quality analysis confirmed the correctness of the proposition for the usage of these progressive control elements.