Something that I see a lot implicitly in the media and the culture is the value placed in the nation as an entity. It is something that I think goes unquestioned, more than most. We often take pride in our nation (though sometimes to satirical extremes, as in 'America, Fuck Yeah!'), but I think that this pride and assumption of the nation state can be dangerous to the health of the citizens.
Over the summer, Russia annexed part of Ukraine, and a big fuss was made about it, talking about how a war might break out over it. Then, there were parts of Ukraine that started fighting to leave and join Russia, though whether that is legitimately Ukrainians wanting to leave, or Russians who are seizing the area, I don't really know or care, and it doesn't matter. The problem is that people are framing the question wrong.
We generally assume that a government is made legitimate by the consent of the governed. Let us assume this to be true. This is a principle that can also be embodied by the idea of the self determination of peoples. Okay, so lets suppose that all people within their national borders are consenting to be governed by that nation, more or less. Clearly in this case, Russia has no claim to invade or annex the people in Crimea, as they have consented to be governed by Ukraine, and not Russia. But suppose those people don't care? They would consent to be governed by Russia or Ukraine? If they are indifferent to who is sovereign, why should the outside world care?
Now let us suppose that they are not indifferent, and would rather be Russian than Ukrainian. In this case, does Ukraine have any right to claim sovereignty over that area after Russia takes it? Sure, Ukraine had it before, but if the people in that region want to be Russian, not Ukrainian, then by the self determination and consent of the governed, they should be allowed to stay Russian. Similarly, if another portion of Ukraine's population wishes to leave Ukraine, what claim does Ukraine have to keep them in Ukraine? If the people derided as 'separatists' withdraw the consent to be governed, then isn't government action against them illegitimate?
Even assuming the legitimacy of all nations, I think these ideas of self determination of peoples and consent of the governed call into question the 'legitimacy' of any civil war, and any nation that engages in such a war. When any portion of a population of a nation withdraws its consent to be governed, waging war against them to keep them in the nation is wrong, by these principles. What ends up as the problem of nationalism is when the people in the rest of the nation support this kind of military action for arguments for national health or power. When we encourage pride in the nation over the consent of the governed, then we lay the ground work for needless civil war.