I'm not sure if these are discussed, but let's talk.
Remember what Mickey said to Data-Sora in Traverse Town before going to Castle Oblivion? Well while in a past like dream version of Traverse Town, you can see Mickey running to the 3rd District door. That probably further proves his statement about being there that day.
Axel and some Nobodies were able to be in the simulated Twilight Town during the prologue of KHII. The reason, it could have been the sigil that was placed in Roxas' name. At least, that's what I assumed, seeing that the X Xemnas showed in front of Roxas looked exactly like the sigil on Sora.
Before the second fight with Demyx, he said "We do too have hearts". Either he thought that was false and was trying to trick the trio he's about to fight, or that he somehow found out that he's been lied to.
How can Destiny Islands be a sleeping world, and awake at the same time? Its not like the one in the tutorial is just in the past. Even if it is, the younger bodies Sora and Riku use can't be sent to Traverse Town and Hollow Bastion respectively after TWTNW. Know what I'm saying?
I'm not sure if these are discussed, but let's talk.
Well that's all I can think of.