Sometimes the karka on the seashore under Owain’s refuge can disappear. It is quite common for one of the karka to vanish each time I go by. I’ve also been ambushed, so to speak, a few times traveling near there so I wouldn’t be surprised if they can suddenly reappear as well.
One time I did have a karka targeted when it vanished. I still tried to shoot it but received an ‘out of range’ message, even though it had been in range before it vanished. The karka was still my target.