They knew what they were shooting, and selected all that made the final cut. BVS was intended to be grim, with its very up-front themes of Superman not acting as God, the mass murder at the hearing, Batman/Wayne's mission to kill (murder) Superman, etc. That's not the CW Flash, or any other lighter material, so if the producers claim they were not trying to be "super serious," then they must have been working on another film at the same time BVS was written, shot and finished. Further, there was a noisy group of fans who complained about how dark BVS (and Man of Steel) was, comparing it to the "lighter" moments or tone in the Marvel movies--Civil War included. They were not complaining for no reason.