Babylon A.D., which evidently made sense at some point, was reportedly disowned by its director over an egregious example of this. The full story can be found here. The studio in question? Fox.
"The film's production was reportedly riddled with problems, from vast delays to budgetary concerns to weather setbacks. Kassovitz points to the studio, 'Fox was sending lawyers who were only looking at all the commas and the dots,' he says. 'They made everything difficult from A to Z.' The last stroke, Kassovitz says, was when Fox interfered with the editing of the film, paring it down to a confusing 93 minutes. Diesel too was astounded at the film's length. Having just completed production of the fourth installment of The Fast and the Furious, he had not seen a cut of the film in six months. 'Am I even in the movie any more, or am I on the cutting room floor?' the actor joked. Fox could not be reached for comment on this story."