The ROM for Kingdom Hearts 358/2 is 256 MB, making it very difficult to copy onto a flashcart with 100% accuracy. When you transferred the ROM file onto whatever data storage device you're using (probably Micro SD), you probably missed a few critical bytes here and there, so that the game freezes in certain spots.
In other words, delete the ROM on your flashcart and copy it over again. Just keep in mind that while it's unlikely the same bytes will be lost, odds are, you'll still have this problem somewhere else in the game.