How do you mean? Do you mean worst as in the film we like the least? Or do you mean worst as in the one with the least technical and artistic merit? Or do you mean which one had the story with the most problems?
Well, if we're talking the one I dislike the least, it's easily Cars, but really, there was nothing technically wrong with it and the story perfectly internally consistent and had no gaping flaws. It just didn't sit with me because I'm not into anthropomorphized cars. Also, I hate Larry the Cable Guy.
If we're talking the film where the plot had the most problems, it would be Up. Up had some fantastic storytelling going, especially where they give you the life of Carl and his wife all without words (it's hard to tell a story without words and get it to have that much impact; regardless of what you thought of the rest of the film, that sequence shows that people at Pixar have talent). Of all the films, Up had the most elements that threw me off. I'm willing to buy the dogs having talking collars for the sake of the surreality of the film, but why were there so many of them? How is there only one bird in the whole area? That's not ecologically possible. How the hell was Muntz still alive? Why did they feel the need to arbitrarily kill off the villain at the end of the film? Why did this film even need a villain in the first place? I kept thinking about these questions and it distracted me from enjoying the film as much as I could have.