On two occasions, when I have teleported to a friend's ship, I end up in the middle of one of the railings that surround him (this was a bison ship, if I recall) and can't move from the point. All I can do is re-teleport.
Also, on a couple of occasions, going from Skull Island Skyway to Flotsom Skyway via the yellow skylane, I come out in the middle of rock, and have to go back to the life fountain.
I have not had this exact problem happen to me, but I have had ones like it where I end up in the wrong place after leaving somewhere. There is a topic called: "floating?" that has more details on these, is that by any chance what you are experiencing?