As part of my thesis about exchange student programs helping overcome prejudices of different culture, I think I should mention these prejudices. I think the biggest ones are religion, historical past and  economical background.

http://religiousaffections.org/articles/articles-on-culture/multiculturalism-cultural-prejudice/
 This article talk about cultural prejudices regarding the religion, where they arise and how to avoid them.

Other conflict I have personally seen was hate among young students from Russia and Germany, students of middle east and american students, russian students and american students or tension between the english and french. I believe though that thru ought the program those people got to know each other and actually become friends despite of history of their countries.