The awesomeness of Mike Bostock's TopoJSON format is not disputable. It drops file sizes by 90% and opens the door to seamless feature simplification. But in the GIS world topology is a fearful thing - it blows up your geoprocessing when incorrect, and "fixing" the errors of features that partially share messy borders can take hours. So I wish the conversion of a messy feature set from .shp or GeoJSON to TopoJSON would magically erase the gaps and overlaps of topological suckage. Would that I could click my heels and make it so, along with a smoked porter appearing on my desk.
This example shows some postal codes at the U.S./Canada border; in 1816 some surveyor-deficient New Yorkers accidentally built a fort 3/4 of a mile into Canada, before realizing their mistake and abandoning it. If the current residents of zipcode 12979 decided they wanted to take that site back, the resulting overlap would be about what you see here, with a U.S. postal code overlapping a Canadian one. This being TopoJSON, the U.S. feature shares a D3 "path" with its New York neighbor. But its Northern border is now unique to that feature, no longer coinciding with the southern path of the Canadian feature it invaded.
This doesn't really pose any showstopping problems in this use case, but it certainly could if the symbology were at all complicated or the label placement were important. My point here is that clean geometry still matters when using TopoJSON; errors don't go away when you make the conversion.