I've countered another strange problem.
Just before fightin' the water dragon under the big canon to help the little girl (middle of Disc 1), I saved and fight the dragon just like the story.
But right before it died, it threw a final attack that make all of my crew died, and, you know, game over.
Then I reloaded my save file and go out to find Yuffie.
Well, the battle with Yuffie begin, and when I won...
I entered the battle with the water dragon right away! WTH? And when I won the battle, the story continued, and I had to search for Yuffie another time.