Question: On the DVD in wide screen, when the flying fish bombard the boat, bigger fish are after them. the bigger fish come out of the normal film area into the black bars above and below movie. How and why did the film makers do this?
Chosen answer: This movie makes a lot of meta-commentary on the medium of digital film; the question of whether Pi's story is real or not mirrors the fact that most of his story is visualized with a green-screen and CGI. The fish leaping "off the screen" plays along with the reality vs. film theme. Plus, they did it because they could, and because it looked cool in 3D.
Question: What exactly caused the ship to go down?
Chosen answer: It isn't exactly clear. Four days out into the Pacific, some noise, possibly an explosion, wakes Pi in the middle of the night. Pi goes out in the midst of a severe storm to explore what happened. Some have suggested that, at this point, he inadvertently leaves a water tight door open which allows storm water to enter the lower levels.
Answer: It's completely up to the viewer to decide. There's no right or wrong answer.