This anomaly is due (primarily) to something called "coefficient quantization." It can happen if you EQ a normalized sound file (even if you're cutting), because you're shifting the waveform around and can wind up generating a new peak higher than the original - which it can't do, so it will distort or "clip." You have to give the EQ (or any effect) a little bit of headroom to work properly. This is no different in the analog domain, although there is usually plenty of headroom in analog to avoid this, whereas a normalized digital file leaves no headroom.