To be fair, Ukrainians typically don't follow a violent and misogynistic religion that refuses refuses to adapt to the modern era.

For one thing, Ukrainians don't come from a region infamous for festering terrorists who could easily exploit refugee waves to hide within their numbers.
For two, unlike the Middle Eastern migrants, Ukrainian refugees are majority female, which does support the idea that they are genuinely fleeing a war and not just moving where the money is. That said, at least in my book you only count as a refugee in the first country that isn't at war, and Japan's pretty far from Ukraine.
Finally, to my understanding, immigration is still a taboo in Japan, and the government started encouraging it only recently to counter Japan's demographic decline.