There's a vast gulf between omniscience and the basic competence to put together a cover story. The mistakes that Hoovaloov pointed out bring to mind Agent J's abortive attempts to make up cover stories on the fly.

It also reminds me of Monster Hunter Nemesis, where the MIB-equivalent shadow organization tried to pin a supernatural massacre in a remote town in Michigan on a mine fire. The cover is pretty much blown when everyone realizes that the local industry is a copper mine, not a coal mine. That blunder was one of a dozen signs that the organization was coming apart at the seams.

Given a choice between incompetence and someone engineering Ben's path of discovery, I hope that it's the latter. The ONI that is competent but driven by a score of conflicting agendas is far more interesting than the ONI that can't keep a clueless prisoner secured on a Dyson shell that they completely own.