There were two static field column in your table billtype and average which needed to be appended before looping the json data

 var outletCount = 0; //global variable to get the no of outlets
var data = [{
    "outlet": "JAYANAGAR",
    "cancelled": 126544,
    "duplicate": 1
  },
  {
    "outlet": "MALLESHWARAM",
    "cancelled": 31826,
    "duplicate": 31
  },
  {
    "outlet": "KOLAR",
    "cancelled": 10374,
    "duplicate": 10
  },
  {
    "outlet": "New Test",
    "cancelled": 154,
    "duplicate": 20
  }
];

let formatData = function(data) { //outlets is unique thats why formating it to loop forward in my code
  let outlets = [];
  data.forEach(element => {
    if (outlets.indexOf(element.outlet) == -1) {
      outlets.push(element.outlet);
    }
  });
  outletCount = outlets.length //calculating outlet count

  return {
    data: data,
    outlets: outlets,

  };
};

let renderTable = function(data) {
  outlets = data.outlets;
  data = data.data;
  let tbl = document.getElementById("tblOlSalesSummary");
  let table = document.createElement("table");
  let thead = document.createElement("thead");
  let headerRow = document.createElement("tr");
  let th = document.createElement("th");
  th.innerHTML = "Bill Type"; //header
  th.classList.add("text-center");
  headerRow.appendChild(th);
  th = document.createElement("th");
  th.innerHTML = "Average"; //header
  th.classList.add("text-center");
  headerRow.appendChild(th);
  outlets.forEach(element => {
    th = document.createElement("th");
    th.innerHTML = element; //this one is populating outlet as header
    th.classList.add("text-center");

    headerRow.appendChild(th);

  });

  thead.appendChild(headerRow);
  table.appendChild(thead);

  let tbody = document.createElement("tbody"); // from here onwards i don't know what to do

  let row = document.createElement("tr");

  let total = 0;

  // static field insertion for Cancelled bill
  let el = 'Cancelled bill';
  td = document.createElement("td");
  td.innerHTML = el.toLocaleString('en-in');
  td.classList.add("text-right");
  row.appendChild(td);
  // Logic start to find the average cancelled amount 
  var total_cancel =0;
  total_can_count = 0;
  outlets.forEach(outlet => { 
    data.forEach(d => {
      if (d.outlet == outlet) {
        total_cancel += parseInt(d.cancelled);
        total_can_count++;

      }
    });
  });

  let el_avg = ( total_cancel / (total_can_count) );
  td = document.createElement("td");
  td.innerHTML = el_avg.toLocaleString('en-in');
  td.classList.add("text-right");
  row.appendChild(td);
  // Logic End to find the average cancelled amount 

  outlets.forEach(outlet => { 
    let el = 0;
    data.forEach(d => {
      if (d.outlet == outlet) {
        total += parseInt(d.cancelled);
        el = d.cancelled;
      }
    });
    td = document.createElement("td");
    td.innerHTML = el.toLocaleString('en-in');
    td.classList.add("text-right");
    row.appendChild(td);
  });

  
  /* console.log("row is : " , row.children ) */

  tbody.appendChild(row);

  let row_duplicate = document.createElement("tr");

  let total_dup = 0;
  // static field insertion for duplicate bill
  let el_2 = 'Duplicate bill';
  td = document.createElement("td");
  td.innerHTML = el_2.toLocaleString('en-in');
  td.classList.add("text-right");
  row_duplicate.appendChild(td);

  // Logic start to find the Duplicate average  
  total_dup_count = 0;
  outlets.forEach(outlet => { 
    data.forEach(d => {
      if (d.outlet == outlet) {
        total_dup += parseInt(d.duplicate);
        total_dup_count++;
      }
    });
  });

  let el_avg_2 = ( total_dup / (total_dup_count) );
  td = document.createElement("td");
  td.innerHTML = el_avg_2.toLocaleString('en-in');
  td.classList.add("text-right");
  row_duplicate.appendChild(td);

  // Logic End to find the Duplicate average  

  outlets.forEach(outlet => { //i am trying to loop through outlets but getting somthing else
    let el = 0;
    data.forEach(d => {
      if (d.outlet == outlet) {
        total += parseInt(d.duplicate);
        el = d.duplicate;
      }
    });
    td = document.createElement("td");
    td.innerHTML = el.toLocaleString('en-in');
    td.classList.add("text-right");
    row_duplicate.appendChild(td);
  });


  /* console.log("row is : " , row.children ) */

  tbody.appendChild(row);
  tbody.appendChild(row_duplicate);

  table.appendChild(tbody);
  tbl.innerHTML = "";
  tbl.appendChild(table);
  table.classList.add("table");
  table.classList.add("table-striped");
  table.classList.add("table-bordered");
  table.classList.add("table-hover");
}
let formatedData = formatData(data);
renderTable(formatedData);

<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.2/css/bootstrap.min.css">
<div align="center" class="table table-responsive">
  <table id="tblOlSalesSummary"></table>
</div>

Get rid of the '#' in getElementById()

let output = document.getElementById("stats-output");

This is an example on how to accept an array of arbitrary objects and just render them on a table by inspecting all of their properties.

Maybe this is an answer trying to address a problem bigger than what was strictly asked anyway it could be interesting to inspect this option.

The main issue with this solution is that, since there's no guarantee on the fact that all objects in the array will be consistent with their properties, the very first step is navigating the whole array collecting a set of unique property names found and use it to build the table header.

Such array of unique property names will be used also later to build the table rows. Since the list of objects doesn't hold the order of the property names, they will be listed randomly in the output table.

The way header and rows get built from the propertyNames and data goes like this:

const header = buildTableHeader(uniquePropertyNames);
const rows = buildTableBody(uniquePropertyNames, data);

The order of items in the uniquePropertyNames will rule how they will be rendered on the output table.

The entry point is just:

renderObjectsToTable(data, '#target');

Where '#target' is the selector to fetch the target table to render the data inside.

Edit: I corrected a mistake I did using the variable data inside a function and I added the demo option to pass a list of html elements to the rendering procedure. Just to draw a bigger picture.

const data = [
  {
    "name": "value1",
    "email": "[email protected]"
  },
  {
    "id": "123",
    "name": "value2",
  },
  {
    "name": "value3",
    "email": "[email protected]",
    "messsage": "lorem ipsum"
  },
  {
    "name": "value4",
    "email": "[email protected]"
  }
];

renderObjectsToTable(data, '#target');
  
function renderObjectsToTable(objects, target){

  const uniquePropertyNames = [];
  objects.forEach(obj => {
    for (const prop in obj) {
      if(!uniquePropertyNames.includes(prop))
        uniquePropertyNames.push(prop);
    }
  });

  const header = buildTableHeader(uniquePropertyNames);
  const rows = buildTableBody(uniquePropertyNames, objects);

  const table = document.querySelector(target);
  table.querySelector('thead').append(header);
  table.querySelector('tbody').append(...rows);
}


function buildTableHeader(propertyNames){
  const headerRow = document.createElement('tr');
  propertyNames.forEach( prop => {
    const headerCell = document.createElement('th');
    headerCell.innerText = prop;
    headerRow.append(headerCell);
  });
  return headerRow;
}

function buildTableBody(propertyNames, objects){
  const tableRows = [];
  objects.forEach(obj => {
    debugger;
    const currentRow = document.createElement('tr');
    propertyNames.forEach(prop => {
      const tableCell = document.createElement('td');
      debugger;
      const value = (obj[prop] === undefined) ? '' : obj[prop];
      tableCell.innerText = value;
      currentRow.append(tableCell);
    });
    tableRows.push(currentRow);
  });
  return tableRows;
}

function goWild(){
  document.querySelector('#target thead').innerHTML = '';
  document.querySelector('#target tbody').innerHTML = '';
  const nodes = document.getElementById('wildList').childNodes;
  renderObjectsToTable(nodes, '#target');
}

#target{
  border-collapse: collapse;
}

#target th,
#target td
{
  border: solid 1px;
  padding: .2em;
}

.hidden{
  display: none;
}

#gowild{
  padding: .5em 2em;
  margin-top: 1em;
  cursor: pointer;
}

<table id="target">
  <thead></thead>
  <tbody></tbody>
</table>

<button id="gowild" onclick="goWild();">GO WILD</button>

<ul id="wildList" class="hidden">
  <li data-wild="very">Wild List Item #1</li>
  <li data-wild="toomuch">Wild List Item #2</li>
</ul>