I think we've had examples of there being Troubled outside of Haven in the past, most recently in the sperm bank episode. Even if the origin of the Troubles is related to Haven, a certain amount of people are going to migrate out, which would spread the phenomenon. Maybe the Troubles started in Europe and Haven was founded as a haven, but then religious fanatics moved in.
As for the bolt-gun killer, there must be more to it than that. The guy in the video was white and had the tattoo.