One thing I just realized that actually breaks the rules that KH set up, by the mid-quel; the Nobodies. It's understood that Kairi's Nobody was formed when she lost her heart, and the 'empty shell' that remains forms it, but in KH1 we see her body with Riku being carried around like luggage. Heck, if I remember right, the scene when Sora stabs himself with the Dark Keyblade, he frees her heart and it goes right back into her, along with the Dark Keyblade disappearing and freeing the OTHER hearts of the Princess', which is another question, but at what point exactly did Namine appear? Also, did Sora just grow a body back from being a Heartless? How did that work? Lastly, shouldn't the Princesses of Heart have Nobodies as well? If Kairi somehow had one, then those other 6 should as well since the only major difference is that instead of their hearts being inside a different person, they were inside an object.
Something else, spoilers for 358/2: [spoiler]Xemnas created Xion through Sora's lost memories, but how did that work out exactly? Did he just force Namine to give him Sora's memories? I can get that she managed to escape the Organization with DiZ/Riku's help, but then how were they also working on restoring Sora's memories at the start of KH2? Did Xemnas just create a copy of Sora's memories then molded them into Xion?[/spoiler]