Their application to the EU has been held up by Greece. The country is caught in a tug-of-war between Bulgarian and Greek claims and disputes and there's an ongoing problem with segments of the Albanian population.
This was a big issue in the early 2000's and could be considered fallout from the breakup of Yugoslavia and NATO's wars against the Serbs. In those wars NATO and in particular the US established very close ties with Albanian elements in Tirana, Kosovo and elsewhere. Albania today is a close US ally, Kosovo is independent under an Albanian government and there's reason to believe the US has backed Albanian insurgents in Macedonia.
As recently as 2015 there have been paramilitary operations in Macedonia by groups such as NLA/ UÇK, which can be viewed as a branch of the CIA-backed Kosovo Liberation Army (KLA). While you cannot draw direct connections and at this point there's no clear documented evidence, there is a certain logic to the attacks in Macedonia, some personnel connections, and certainly historical precedent.
There are many issues at work here, the stress within the EU, Right-wing Nationalism, energy, pipelines, Russia, and certainly some larger questions with regard to Turkey, weapons and drugs smuggling, terrorism and Syria. It's complicated and it's hard to get good news on the region and its complex internal politics, but it's clear there are forces at work and looming trouble.
Not every link is totally reliable but there are numerous points of interest and items to be gleaned and considered.