My hypothesis for both this and most of the things stated in the article: the EEG machine itself is picking up the fluctuations in its EM environment.

I mean, what's more likely - that the binaural beats retune brain, or that someone forgot that any straight-ish piece of wire is a radio antenna, and the signal being seen comes straight from headphones? Using pneumatic headphones would make it go away too.

I wonder if they tested by running the experiment without a human in to get a baseline measurement.