There were two speculations in the article, that Bleach Bit didn’t work and that the FBI gained access to the recipient’s accounts and those were not scrubbed.
Smart employees make a copy and take it with them if there is the slightest hint they could get into trouble. If there had been an indictment those hard copies would have appeared, probably killing a whole forest for the paper.
It's not Hillary's job to keep tabs on all the computers....but from what I gather, she doesn't like people around... she used what was available.