"if we go to the capital after we have the rock , we will enter to the map and still stuck there with no possibility to get out"
I noticed this just the other day, while coding one of the new events for version 0.9, it's now fixed (for version 0.9)
Thank you for the report ;D
As for the save file, I'm not sure how it works, but RPG Maker MV uses multiple files for saves:
config.rpgsave
global.rpgsave
file1.rpgsave (the number on this one depends on the save file, obviously.)