Fans at the game and television viewers were likely aware of the absence of El Batallon in the stadium during the DC United match. Apparently, two members of the group were caught burning a flag during the FC Dallas match on May 5th and the group chose to boycott the match over what I assume were issues with how security handled the incident. There really isn't any more details than that, though Glenn Davis has some thoughts on the issue which I encourage everyone to read.
Whatever your feelings about El Batallon, their passion and sound is a huge part of the Robertson Stadium experience and even though Texian Army did well on Saturday, it's always better for the stadium to be in full voice.
If you are a part of El Batallon and would like your side of the issue presented, feel free to contact me: zach [at] dynamotheory.com