Minorities played a significant role regarding the security of Europe primarily in the period between World Wars; unfortunately, they often directly endangered many countries. The situation in the EU is different today; however, the risk of potential conflicts should not be overlooked, such as in Spain.
The new issue is gained with strong immigration, when new minorities are emerging. But the revival of traditional minority conflicts may also affect the EU, as shown by the Crimea and Eastern Ukraine, but also currently Catalonia.
Even worse could be the activation of traditional German and Hungarian minorities in Central Europe. Such cases have been extremely demanding for the security forces of any country.