Just arrive to Skellige and for some reason the game won;t allow me to save it, it autosave whenever I transport from location and it autosave at checkpoints but won't allow me to manually save. I don't encounter that kind of problem in any other area of the game.

Does it also successfully autosave after a certain amount of time played ?
Do you have enough hard drive space ? Maybe your drive is full. I think there's a limited number of autosaves and the game keeps replacing the oldest ones so they don't need extra space but every manual save creates a new file.
Did you try to maybe spam the quicksave button ? Doesn't really solve anything but at least lets you save where ever you want for the time being.
Can you do stuff like alchemy or changing your activated skills ? Maybe a bug put you permanently in 'combat' state ?

Restart the game and now it save just fine, but sometimes it still don't allow saves. weird.

You cannot save while Geralt is moving, maybe that causes the issue.