You aren't specific in your question, but it sounds like you're using an onEdit trigger function to set a "last updated" column.
Just check if the current row is within the header, and exit the trigger. Something like this:
function onEdit(e)
{
var rr = e.range;
var ss = e.range.getSheet();
var headerRows = 1; // # header rows to ignore
if (rr.getRow() <= headerRows) return;
...
Here's your onEdit, after combining with the suggestion above. In one of these trigger functions, you want to invest as little as possible before checking whether you should bail out. You'll note that the check for headers is at the top of the function, for efficiency. Unnecessary lines have been commented out, for the same reason.
function onEdit(event) {
// note: actRng = the cell being updated
var actRng = event.range;
var headerRows = 2;
if (actRng.getRow() <= headerRows) return;
var sheet = actRng.getSheet();
//var index = actRng.getRowIndex();
//var cindex = actRng.getColumnIndex();
var dateCol = sheet.getLastColumn();
var lastCell = sheet.getRange(index, dateCol);
var date = Utilities.formatDate(new Date(), "GMT", "MM-dd-yy");
lastCell.setValue("'" + date);
}