The runner was not impeding the fielder. The fielder changed direction TO GET TO THE FLY — not because a runner was in his way. The fielder misjudged the ball at first. After he located the fly, he changed direction.
Even if the runner was aware of where the ball was, he would have had no reason to think he was in the way because HE WASN'T.
And the 3B umpire didn't know where the ball was either when he first makes the call. If he'd have waited, he would have seen the fielder changed direction because he FOUND THE BALL in flight and adjusted his path.