There are multiple possible explanations. First, i don't know if MC catches intersample peaks. If not, that would be a good explanation. By attenuating a frequency you could move a peak to a sample that wasn't on a sample but between two samples.
Secondly, by attenuating you can actually increase the peak volume. This is clearly visible when altering a square wave.
Thirdly, I don't know how the EQs are implemented, but some EQs actually boost the frequencys a bit around the cut.
And last but not least, if you have downmixing of multichannel audio and are cutting a frequency before downmixing, you are altering the interference. Maybe there were Peaks that were destructivly interfering and by lowering e.g. 50Hz on the LFE the peak on the Left channel now interferes constructively as the phase was shifted.
To make sure you don't get clipping you could apply a adjust volume on all channels with -2dB. That should cover almost all most cases, as intersample peaks usually are below +1dB. I had very rare cases where I needed to lower the output by 6dB, but I also have some extreme EQing going on, so -2dB should be fine.
