D3 is not mistaken, the data is incorrect, and the leaflet is more lenient.
Take Lichfield (upper left district) as an example:
{ "type" : "Feature", "properties" : { "kind" : "county", "name" : "Litchfield", "state" : "CT" }, "geometry" : { "type" : "MultiPolygon", "coordinates" : [ [ [ [ -73.0535, 42.0390 ], [ -73.0097, 42.0390 ], [ -73.0316, 41.9678 ], [ -72.8892, 41.9733 ], [ -72.9385, 41.8966 ], [ -72.9495, 41.8090 ], [ -73.0152, 41.7981 ], [ -72.9823, 41.6392 ], [ -73.1631, 41.5571 ], [ -73.1576, 41.5133 ], [ -73.3219, 41.5078 ], [ -73.3109, 41.4694 ], [ -73.3876, 41.5133 ], [ -73.4424, 41.4914 ], [ -73.4862, 41.6447 ], [ -73.5191, 41.6666 ], [ -73.4862, 42.0500 ] ] ] ] } }
The multipolygon is not closed, its end is not equal to the beginning. I built the coordinates, indicating the first coordinate of red, and the last green - 
As you can see, the last coordinate is discarded by d3.
GeoJSON specification says
A LinearRing closes a LineString with 4 or more positions. The first and last positions are equivalent (they represent equivalent points).
So, d3 has a point (not intended for pun intended), and MultiPolygon should be closed by adding the initial coordinate to the end:
...[ -73.4862, 42.0500 ], [ -73.0535, 42.0390 ] ] ] ]