Yankees-Jays (batter hit on strikeout)

[Jay R]

In yesterday's (Sunday) ballgame, Jays pitcher Roy Halladay struck out a Yankee (I can't remember who) and he was hit in the foot with the pitch. R1 and R2 both advanced on the play and the batter was called out. (There was one out).

I was expecting the umpires to discuss the play and send the runners back. They didn't. Jays manager Cito Gaston came out to talk to the HP umpire but the discussion was brief and Gaston was not overly upset. The idiot announcers (Jays broadcast) discussed it. One said:"Is the ball dead when it hits the batter?" The other said:"No the runners can advance at their own risk"

I'm wondering if the umpires blew the call or if the HP umpire never saw the ball hit the batter's foot and just called strike three and a wild pitch. Did anyone see this play and have any thoughts. Am I missing something here?