Supporters' Shield winners Galaxy saluted 1-0 thanks to Mike Magee's 15th minute goal but scenes involving Landon Donovan and Rafael Marquez, plus others, at the final whistle have dampened the encounter.
Ex-Barcelona star Marquez threw the ball at Donovan right on the final whistle with the USA international's teammate Adam Cristman coming to his defence before Juninho and Red Bulls defender Stephen Keel also got involved.
The Red Bulls were clearly in the wrong with Marquez' petulant act and the actions of the home team have been criticised by Donovan.
"I saw it and I think Adam [Cristman] saw it as well. So Adam was sticking up for his teammate," he said.
"There a few plays where they took some cheap shots at us. In all my years in this league, I've not played against a cheaper team, and they've been doing it all year.
"We saw it a few weeks ago with [Thierry] Henry kneeing someone in the back. We've seen that stuff all year.
"You just deal with it, and at the end of it, the cream rose to the top, and the better team won."
Following the game, Marquez and Juninho were suspended for the return leg on Thursday night - Marquez for his huffy act of throwing the ball at Donovan - and Juninho for elbowing Keel in the mouth as he was simply trying to keep the peace.
The clash after the match will certainly make for an interesting return leg at the Galaxy's The Home Depot Center this Thursday with LA holding a slender lead as they look to qualify for their second MLS Cup final in three years.