You aren't using a projection - so the coordinates in the file are translated to pixels with no transformation. If your data has typical geographic coordinates, or lat longs that are both positive, high values are at the north end (the top in most maps), and low values are at the south end (the bottom in most maps).
In svg coordinates, low values are located at the top and increase as one moves towards the bottom - the opposite of most geographic coordinate conventions. You could use a geoIdentity as your projection to flip the json's y coordinates:
var projection = d3.geoIdentity()
.reflectY(true)
.fitSize([width,height],geojson)
Where geojson is your feature collection: topojson.feature(us, us.objects.counties)
And then use it with your path:
var path = d3.geoPath().projection(projection);
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