non linear EQ creates distortion by introducing a phase shift in frequencies, in a non-linear manner, so one frequency may shift by 0.002m, and another 0.01m, which means the waves start to overlap, it can result in cancellation (silence) or significant resonance (ringing) between frequencies, this happens across the spectrum, but sub is the most likley place you will notice it at first because of the long wavelengths. If two peaks overlap, they will resonate, ring out, if a peak and a trough overlap, they can cancel each other out and cause silence or reduced amplitude/volume.
A linear phase EQ, removes this problem, there is still a phase shift, but all the frequencies are calculated to have the same phase shift (a linear phase shift across the spectrum), which means that relative to one another, all the frequencies are still in the same phase as they where pre-processing - linear phase also introduces a slight delay/latency, because of the phase calculations, sometimes this is a pre-delay, so things get shifted backwards, sometimes post, so the delay extends after the sound, the timing is minuscule, and how much you notice it depends on the EQ, it can be quite a pleasing sound
Sometimes non linear phase distortion from EQ's can be musical, there are many EQ's which 'color' sound in this way and it sounds great, but sometimes it is not good at all, sub being one of the biggest problem areas.
