The flag was found outside of the Jewish student group's office door on Tuesday. The flag had the word "terrorists" scribbled on it.
"I would want to know what they were hoping to get out of that," said Danny Leserman, a member of Highlanders for Israel.
The act also saddened Shadi Matar, who is part of the group Students for Justice in Palestine.
"I'm shocked and to be honest, just disgusted by it, I think an act like that or vandalism is frowned upon in any sphere you come from," Matar said. "Whatever point you are trying to get across, this is the wrong way of doing it, there are better means to get your point across other than vandalism."
This is the latest in a string of tensions between Muslim and Jewish students at UC campuses across the state.
There have been recent incidents at UC Davis, UC San Diego and even UC Irvine two years ago, where a group of Muslim students disrupted a speech by the Israeli ambassador.
UC system president Mark G. Yudof released a statement Thursday about the vandalism, saying: "There inevitably will be speakers or forums that present ideas others will view as hateful and abhorrent. Hateful incidents will not be tolerated and I stand ready to condemn them whenever and wherever they occur."
Leserman feels these conflicts are no longer a surprise.
"Tensions have always been at an all time peak, it's nothing really new," Leserman said.
But it is something Leserman and Matar are trying to change. They are working together to try to open a Middle Eastern student center. They both hope that even though there may always be disagreement, understanding may someday happen.