I think the center func offset in axis.js is slightly off.

function center(scale) {
  var offset = scale.bandwidth() / 2;
  if (scale.round()) offset = Math.round(offset);
  return function(d) {
    return scale(d) + offset;
  };
}

Suppose bandwidth is 3. Then we expect the offset to be 1, to place it on the middle pixel. With the current implementation, you would get 1.5 or 2, depending on the rounding flag. I think the correct offset should be:

var offset = (scale.bandwidth() - 1) / 2;