For one, it goes by "per capita". That is why a place like Camden (1) is more dangerous than a place like NYC (256).
For two, the criteria they go by is a bit skewed as well. It includes: "murder, rape, robbery, aggravated assault, burglary, and motor vehicle theft." This may include things like domestic violence, as that is considered "assault". So there may be 50 murders in Fresno, but there might be 40 assaults and 50 burglaries, and 30 cases of domestic violence in Anchorage.