If a plot specifies an inset as well as axis marks, then the resulting height causes y labels to overlap if the data only produces two bands:
Plot.plot({
  inset: 20,
  marks: [
    Plot.axisX({anchor: "top"}),
    Plot.axisX({anchor: "bottom"}),
    Plot.dot("AB", {y: d => d, x: 0})
  ]
}) 
Screenshot:
