According to a report from Hollywood Reporter, this film ended up being plagued with issues from the start.
Warner Bros only gave them about 6 weeks to write a script. The director only got picked because other bigger name directors either refused or were already busy on other projects. Only reason reshoots happened was due to the boss of Warner Bros being pissed at Batman vs Superman "damaging" their DC film brand.
In regards to comedy in the film, Warner Bros wanted more added in while the director and actors didn't.
http://www.gamespot.com/articles/sui.../1100-6442334/