Sales Order Entry Shipping Instructions are changed when the order ships

We entered a sales order with FedEx Ground Collect and the customers account number.  However, the invoice generated in the shipping batch shows Collect terms with a shipping charge and a UPS tracking number.  I was told Sage changed this.  Is that possible?  If so, how and why?  Is this a data entry error or is there some setting in Sage that did not save the shipping instructions?