Error adding N elements with Javascript

The detail you have when calling the function Calcular ; the value before the modification is not being subtracted from Total (at the end of the table) you are only adding the new value (of the modification).

I suggest you perform the calculation of all existing elements (practically go through all the elements and get the totalitem and add it, or add a new parameter to 'Calculate' in which you pass the value that you had before its modification for subtract it to end up doing something like:

total.innerHTML = parseFloat(total.innerHTML)+totalitem-valorAntesModificar;

Do the following to add to your code:

Modification to function AddItem :

function AddItem() {
    var tbody = null;
    var tabla = document.getElementById("tabla");
    var nodes = tabla.childNodes;
    for (var x = 0; x<nodes.length;x++) {
        if (nodes[x].nodeName == 'TBODY') {
            tbody = nodes[x];
            break;
        }
    }
    if (tbody != null) {
        var tr = document.createElement('tr');
        tr.innerHTML = '<td><input type="text" name="item[]"/></td><td><input type="text" name="cantidad[]" onChange="Calcular(this);" value="1" /></td><td><input type="text" name="precunit[]" onChange="Calcular(this);" value="0"/></td><td><input type="text" name="totalitem[]" readonly /></td>';
        /// agrege la siguiente (por la estructura que usaste; aquí guardo el valor anterior
        tr.innerHTML+='<td style="display:none"><input type="text" name="totalitemold[]" value="0" /></td>';
        tbody.appendChild(tr);
    }
}

Make changes to Calcular :

  function Calcular(ele) {
    var cantidad = 0, precunit = 0, totalitem = 0;
    var tr = ele.parentNode.parentNode;
    var nodes = tr.childNodes;
    // Inicio: Lo tenias casi al final
    var total = document.getElementById("total");
      if (total.innerHTML == 'NaN') {
          total.innerHTML = 0;
      }
    // Fin: Lo tenias casi al final

    for (var x = 0; x<nodes.length;x++) {
        if (nodes[x].firstChild.name == 'cantidad[]') {
            cantidad = parseFloat(nodes[x].firstChild.value,10);
        }
        if (nodes[x].firstChild.name == 'precunit[]') {
            precunit = parseFloat(nodes[x].firstChild.value,10);
        }
        if (nodes[x].firstChild.name == 'totalitem[]') {
            totalitem = parseFloat((precunit*cantidad),10);
            nodes[x].firstChild.value = totalitem;
        }
        if (nodes[x].firstChild.name == 'totalitemold[]') {
            total.innerHTML = parseFloat(total.innerHTML)-parseFloat(nodes[x].firstChild.value,10); // Restamos lo anterior
            nodes[x].firstChild.value=totalitem; //  Asumiendo no hay falla se coloca el nuevo valor de "if (nodes[x].firstChild.name == 'totalitem[]')", el cual será el "valor antes de modificar"
        }
    }

    total.innerHTML = parseFloat(total.innerHTML)+totalitem;
}

Notes: