From the Astros' website:
Crew chief Randy Marsh, who was umpiring at first base, told The Associated Press after the game that both he and Wendelstedt saw Munson touch the ball and cause it to go out of play. That meant Cabrera was awarded two bases from the time of the pitch.
But Munson said he never touched the ball before it disappeared into the dugout. If that's what happened, Cabrera should have only received one base.
"I don't even know where the ball went," Munson said.
Here's what I can find in the official MLB rules is this, found in section 7.05:
Each runner including the batter-runner may, without liability to be put out, advance -- (edit edit edit)
(h) One base, if a ball, pitched to the batter, or thrown by the pitcher from his position on the pitcher’s plate to a base to catch a runner, goes into a stand or a bench, or over or through a field fence or backstop. The ball is dead;
APPROVED RULING: When a wild pitch or passed ball goes through or by the catcher, or deflects off the catcher, and goes directly into the dugout, stands, above the break, or any area where the ball is dead, the awarding of bases shall be one base. One base shall also be awarded if the pitcher while in contact with the rubber, throws to a base, and the throw goes directly into the stands or into any area where the ball is dead.
If, however, the pitched or thrown ball goes through or by the catcher or through the fielder, and remains on the playing field, and is subsequently kicked or deflected into the dugout, stands or other area where the ball is dead, the awarding of bases shall be two bases from position of runners at the time of the pitch or throw.
So that's what the ump crew is basing their ruling on, but as far as equipment might concern that fiasco last night, all I could find was this:
3.14
Members of the offensive team shall carry all gloves and other equipment off the field and to the dugout while their team is at bat. No equipment shall be left lying on the field, either in fair or foul territory.
So if the on-deck circle is in foul territory...