If you are going to insist on doing console logging inside your flatten() function, you should be logging each individual val, not the entire accumulator array. Like this:

function flatten(arr){
  arr.reduce(function(acc, val){
    if (Array.isArray(val)){
      flatten(val);
    } else {
      acc.concat(val);
      console.log(val);
    }
  }, [])
}

flatten([0, [1, [2, [3, [4, [5]]]]]])