I think the idea they tried to convey with the refugee camps is that they fear the Japanese because of their association with the Britannians, similar to how WWII-era USA treated the Japanese Americans. It wasn't too clear, obviously.
You can see that this is untrue by simply observing how they treat different characters in the show. Leila is also an exile, in fact her family was exiled from Britannia, a noble family from the enemy empire itself. They should be treated with even more fear. But no, they are welcomed, their children adopted into power families, they've viewed with interest and not disgust, and they can grow up holding leadership roles in the military.
Meanwhile the Japanese? They looked down upon, rejected, used as canon fodder, and even military drivers don't like them. Commanding Officers make comments about how their lives are useless, talk shit about how they're only good as KAMIKAZE, and nobles see them as brutes who know SCARY ASIAN NINJA SKILLZ. The displaced refugees are fenced off, they're not well looked after, and they all have this sad resigned look on their faces.
And all this is set in a world where the Japanese were never at war with anyone, there is no America, there was no Pearl Harbor, and there is zero reason for anyone outside of Japan to have this ultra xenophobic racist viewpoint of the Japanese people.
So how do we explain it? Is it really just bad writing? I don't think so. In fact, I find the refugee situation in Akito very familiar. I've seen it before. In anime even. Where? Ghost in the Shell: Stand Alone Complex. The story, especially in the second season, depicts a future Japan with a refugee problem due to conflict in the surrounding Asian region. Refugees are displaced into Japan, and the people in Japan hate it. This is natural and realistic because Japan by nature is a xenophobic closed nation. Foreigners are viewed differently, and refugees are foreigners who have no "good" reason to be in the country. This becomes a social problem.
Since Akito is a Japanese anime production intended for a Japanese audience, created by Japanese staff, it is not really that surprising that their viewpoint would be extremely Japanese in nature. So even when they are dealing with a story which supposedly takes place in Europe, and the refugees are Japanese, while the country in question are filled with Europeans (which in this case seems to basically be Generic White People), their perspective of how refugees of a different ethnic group would be treated is based on their personal view of how a situation like this would play out in Japan.
That's how I see it. Seems to make sense to me.
