The last line of the file was empty, so [a, b] was destructuring to ["",undefined]. I just added a filter.

const coordinateListString = await Deno.readTextFile("input.txt");

let aSetBCoordinateList = coordinateListString
  .split("\n")
  .filter(line => line !== "")
  .map(str => str.split("   "))
  .map(([a,b]) => [new Set([...a].map(Number)), b.split("")]);