Maybe you should change the format or adjust the sound quality by adjusting the bit rate, sampling rate, etc.
If that doesn't work, maybe swithcing to another audio capture called TunesKit Audio Capture? It is able to record the audio in 6 different formats without quality degradation, so it might solve the problem. At least, I haven't heard strange noises in its recordings during my last 2 months usage.
Hope it helps.