I have found the cause as if we have Blank Cells or Merged Cells in the First row of template and uploaded File it is not able to compare and it trowing column header mismatch. It works only of cells are not merged and should not be blank.
So if Pega can fix this it will helpful for future validations. Also currently it is hard coded inside the function to check for only 1st row as header. Instead they can provide a param to consider how many rows as headers. So that accordingly can be validated for header rows