I'm not sure where I read it, but I think this plays into the Bennett plotting thing of suspense vs surprise, and the idea on TFF was that they were doing a lot more surprise early on - one of those ideas being surprise the ship doesn't work.
But in terms of WHY it doesn't work - got no idea. It would have been great if it were a plot point later in the film ... y'know, klingons try to board the ship and get stuck in the elevator, or something equally stupid but justified by what has gone before. But instead the ship seems to 'get better' as it goes along. Maybe it just needed to be out of Sol system to straighten up & fly right.