I'm seeking terms that emphasize a distrust or misunderstanding between ingroups and outgroups. There are a few issues I have with using xenophobia.
Xenophobic groups tend to be rather large and fairly general. Think mainland Japanese vs. outlanders or USA vs. Middle East. (Yes, I am making broad sweeping generalizations. That's the point.) What if I want to indicate mistrust between members of similar communities, who nevertheless have differing cultural traits? Examples: soldiers vs. citizenry, religious vs. secular, gun-owners vs. anti-gun supporters. Those are heavier examples. As a lighter one, consider a word that can generalize xenophobia to how subcultures like heavy metal fans were viewed by suburbia in movies like Detroit Rock City.
The suffix phobia is fixated on fear and dislike, not necessarily distrust and misunderstanding. Perhaps these are similar in meaning, but I am slightly dissatisfied.
Related words, such as some in this post, tend to be focused on negative personality flaws (e.g. bigotry). Xenophobia doesn't cast that same light. It's, how to say, more clinical or academic in its diagnosis.