How to make bode plot when output signal changes amplitude?
You are probably still seeing other frequency components from the transient of the system. I assume you that you simulated your system for a fixed number of periods of the excitation signal. If this is the case then it would also explain why you only see the transient at high frequencies. This would be because a fixed number of high frequency periods take less time than the same number of low frequency periods. Therefore there is not enough time for the transient to die out for the high frequency excitation.