Why was this case tried in a military court?

It's Russia's turn. The Baltic Fleet Military Court in Kaliningrad Oblast has convicted three civilians whose offense was that they would like the Baltic enclave to be able to cooperate with the European Union. MediaPart has the story. Excerpt:

Initially, the activists were accused of intending to take power in the Kaliningrad region to join the European Union. They were charged with extremism, but then the case was reclassified to a much more serious charge: organizing and participating in a terrorist organization. They were involved in the distribution of leaflets containing "indications of incitement to violent actions against [Russian President Vladimir] Putin".

Watch for a complaint to be lodged with the European Court of Human Rights following the exhaustion of national remedies. Human rights jurisprudence strongly disfavors the exercise of military jurisdiction over civilians.