It is an old myth that the nation-state is a major source of trouble. And in Europe the EU has been brought as a solution of that problem.
In fact the nation state is a logical consequence of modernization. In modern society in most jobs language proficiency is needed and as a consequence people pay a major price when they will in a country where the national language is not their mother tongue. Another facet of modern life is that most people are employed by some organization. This makes them vulnerable to discrimination. Most nation states follow indeed linguistic borders and where that is not the case there is often a history of discrimination.
In fact the trouble caused by the rise of the nation state is mainly friction trouble. Every change causes winners and losers and the transition towards a nation state is no exception. When you have border changes there is always one party losing something. And when you have new borders there are always some people who suddenly find themselves on the wrong side of those borders.
As Europe has mostly been through this phase of transition its nation states are no longer a source of trouble but rather a source of stability. Sure, there are still some trouble points - mainly in the East - but we have established sound procedures to handle them (for example with the Helsinki Accords). When problems do arise - see Yugoslavia - it is because we blatantly ignore those rules.
This brings me to the EU. One can have different ideas about its viability as nowhere else in the world one can find a similar super state. But one thing is sure: the road towards European unity is change and change causes friction and possibly war.
Initially the EU was mainly a cooperation between nation states that allowed these nation states to function better in world where some of their markets were too small to allow sound competition. But in the last decades the EU has become a power in itself that actively tries to dismantle the nation states. And since then it has become increasingly a source of trouble.