I remember years ago, when I learned from a trans friend how the trans community has such nasty conflicts. I'm talking, way worse than the atheist community. Transgender people and intersex people didn't get along, trans men and trans women were always clashing heads. And then there are factions of "classic" transsexuals who disidentify with "transgender", and who deride transgender people as crossdressers and autogynephiliacs. There are also actual crossdressers who get beaten up by everyone.
Don't take my word for any of this, all my information is probably out of date. But I had the strong impression of great internal conflict. It seems to correlate with the great amount of oppression experienced by trans people. This just begs for a general theory: External oppression of a group causes internal conflict.
This would be difficult to prove, since it would require many subjective judgments about how nasty internal conflicts are, and how oppressed different groups are. Let's not even go down that route. Let's talk about mechanisms and consequences instead.
Here's one example of a clear mechanism. I heard a friend talk about how he was openly gay in high school, and how so many classmates derided his masculinity for this. Then there was another gay student who was actually very effeminate, and he hated that guy for proving stereotypes right (now he knows better). The femme guy, however, hated the butch guy for enabling the bullies. A simple stereotype divided them into those who confirmed the stereotype, and those who did not.
There's another phenomenon, where people have strongly negative reactions to some attitude, and adopt a dogma in response. Internal conflicts among feminists show many examples of this. The prominence of abortion makes many people think feminism is about choice (but it really isn't). The prominence of rape culture makes many people say that rape is about power (but it isn't just). I do not mean this as a criticism of feminism, but as an illustration of how we are all fallible.
I also recently observed that as a person of color, I often feel uncomfortable about criticizing other people of color who speak about race. This is due to a culture of suppressing criticism. But that culture is there for a reason, and that reason is that there are many many people who don't have a very deep understanding of race, and yet will dominate any critical discussion about race. To avoid all the vacuous critics, people are always on edge about any critics, because there just isn't an easy way to distinguish vacuous critics and helpful critics (and not even the critics know which ones they are, not even I know).
These are just three mechanisms. I welcome more ideas.
I propose that this is one of the reasons why social justice communities have a bullying problem.
But I cannot propose a solution. There isn't really an escape in sight. We can't just tell people to be nicer to each other, because the problem isn't just that people are mean. Often, external oppression precipitates problematic attitudes within the community, and these problematic attitudes are worth being angry about.
Solving this problem would be akin to solving the problem of human conflict in general. So unfortunately, I think we're stuck with it.