2 outs, and Hairston was on first. Batter hit the ball, it hit the pitcher's glove, then rolled past him towards the second baseman. Hairston was running to second, and he ran between the ball and the 2nd baseman, who rushed up to grab it. Hairston got to 2nd base, and the runner ended up being safe on first.
Umpire called Hairston out for interference with the 2nd baseman. It is questionable because the pitcher initially touched the ball, so it can be argued that since he had had a chance to field the ball, then it shouldn't matter.
Anyway, it makes sense if you watch the replay.
So Bud Black told the ump that the Padres were going to play the remainder of the game in protest. I read up on what that means, and basically, the manager can say the game is under protest if he disagrees with the ump's ruling. At the end of the game, the rules will be reviewed by a committee, and they can overturn the ump's call or say it stands.
If the call stands, that's that. If the committee overturns the call, the game will be replayed from the point in the game that the protest call was made.