The skip scene feature in KHFM is nothing like the skip scene feature that we're all used to in every other KH game. It only lets you skip the scene if you have already viewed it in that particular save file. This means that you still cannot skip scenes the first time you get to them. you only can if you die against a boss and try the fight again immediately. Also, even if it is your second time watching a scene, you cant pause and skip the scene mid way through. It asks you if you want to skip at the very beginning of the scene and if you say no, you must watch the whole thing.
Hopefully, they rework the skip feature to be like it is in all other titles.