Ok, I went to your git repo, but since you don't have the whole project there I can't exactly download and try it out on my own, but my advise to you would be to put a "Debug.log()" inside your Jump() method and then go back to the editor and try to jump a few times and check if that call is not triggering more than once, that would be my first guess. If so, you could make a global bool "canJump" and in place of calling Jump() in the update method you would set that bool to true, and then in the FixedUpdate() you would say if(canJump){ Jump(); }
I'm not sure if that solves it, but you could try it.