Stuck at Floating Continent

I used the Auto Battle in the Lethe river to level up, Cloud stayed with that level because he was already in the party and the characters that were joining had the average level

Ahh I see, gotcha. Looks like I never did put back level averaging for Cloud where I had removed it long ago. I will be sure and put that back in the next update!
But yeah, Cloud still shouldn't have access to Limit Breaks 5 and 6 until level 25 and 36 respectively, so something definitely wrong with that - I mentioned about there being a bug in the previous version before 2.7, where it could/would do just that for Cloud and Ronan, give them skills that they shouldn't yet have, it was due to a bug with a custom event command... anyways it could cause some nasty issues besides this we think, and the npcs being gone from the floating continent somehow might be related. I'll have to see if that bug is still present in this version, as it looks like it is for your save file... Besides that I'm not sure at all, I was leaning towards it being a max npc issue, but it doesn't seem like it since my save data it doesn't happen and this has never been reported.