Umpires train themselves to watch the feet while listening for the ball to hit the glove.
In this case, however, the toss was to a pitcher covering first base, and the ball wasn’t thrown far; so the umpire might have been watching the ball.
I woudd really like to see a video that doesn’t stop as the runner hits the bag. That pitcher’s foot might be coming up, not down.
http://mlb.mlb.com/video/play.jsp?content_id=8616789
It’s not coming up. It’s really inexplicable. It’s not even a close play. But, as the pitcher said, people make mistakes. It’s just weird.