I’ve only had this occur once so far, but it was enough to make me rage quit on my current progress (5 days lost).
I was flying to one of the islands after moving my shelter to the central island and the game paused halfway across the ocean whilst I was in mid-air; the sound was still playing but the screen froze.
When the screen unfroze, I was swimming in the middle of the ocean, my gyrocopter had gone, I had to swim back to my home island to process what I was doing.
I don’t recall if I was swimming between a custom to custom island or a custom to game generated island. But the freeze occurs everytime I travel - that now I just keep tapping on the hover button to keep me in the air; but considering that I cannot see where I am, or what direction I’m facing as I try to hover - it’s a worry.