commented-version.js

var fs = require('fs');
var path = require('path');

// fs.readdir is an async func, it doesn't return any value 
// see: https://nodejs.org/api/fs.html#fs_fs_readdir_path_options_callback
// var lists = fs.readdir(process.argv[2], callback);
fs.readdir(process.argv[2], callback); 
 
 
// it yields just a single list, not lists. That list is in fact an array
// function callback (err, lists) {
function callback (err, list) {
  if (err) {
    throw err;
  }

  // it is fine to redefine the variable, however, for clarity you should put it on a new var
  var filtered = list.filter(function (item) {
    // 
    return path.extname(item) === '.' + process.argv[3]
  })
  
  // You don't want to call the callback inside the callback, it will just make the function recursive
  // Just like your previous solution, you just need to print the result (filtered list)
  // callback(null, list)
  console.log(filtered)
}

fabio-version.js

var fs = require ('fs');
var path = require ('path');

var lists = fs.readdir (process.argv[2], callback);
 
function callback (err, lists) {
  if (err) throw err;

 lists = lists.filter(function (list) {
    return path.extname(list) === '.' + process.argv[3]
  })
  callback(null, list)
  
}

solution.js

var fs = require('fs')
var path = require('path')

var dirPath = process.argv[2]
var ext = '.' + process.argv[3]

fs.readdir(dirPath, function (err, list) {
  if (err) { throw err }

  list.filter(function (item) {
    return (path.extname(item) === ext)
  }).forEach(function (item) {
    console.log(item)
  })
})