Some films, such as The Good Dinosaur have seen entire movies basically canned after it was decided that the existing story just didn’t work.
The story is always something that is perpetually worked on during the production of a Pixar film, it’s never entirely finished until the whole movie is done.
While the difficulty with the script may be cause for alarm for some fans, it really seems like the actors feel Pixar has nailed it, so perhaps the extra time that was taken to get the story just right was worth it.