The merchants reference is a unique value that you must send along with each goal. Usually this would be a 'transaction id' or 'order number'. You should have a methods of tracing this reference back to your own records.
If the goal doesn't relate to a transaction that has a unique reference you must create one for the purpose of correctly tracking commission.
If you send a reference that has already been recorded by Aflite your goal will fall into error and affiliates will be notified that there are tracking issues.