I don't think there's any need for a cui bono line of thinking. There are biologists who have nothing to gain who thought this paper was lousy. For example, every single biologist in my department that I spoke to, and every biologist I've found online who had something to say on the matter.

Perhaps that's too much of a selection bias for you, so I'll offer this critique: if you wanted to measure the off target effects of Cas9 in an organism, you would probably sequence the organism before you edited it, and then sequence it again after you edited it. But that's not what they did.

Also refuted by a team from Harvard medical school:

http://www.biorxiv.org/content/early/2017/07/05/159707