Excerpt shows they used non-government phones part of the time to hide their communications:
http://www.foxnews.com/politics/2017/12/13/ex-mueller-aides-texts-revealed-read-them-here.html
04/02/2016
Page So look, you say we text on that phone when we talk about Hillary because it cant be traced, you were just venting, bc you feel bad that youre gone so much but that cant be helped right now.
I am venturing to guess, that raised some eyebrows since the Hillary investigation was still underway on Apr 2.