Is there an area in the sales order where notes can be entered to keep track of customers with problems with the product they received?

There are both internal notes and external notes (can be seen by the customer) for the purposes of order tracking and improved customer service. Both sets of order notes are always trackable throughout the entire order fulfillment and RMA processes. These notes are presently not posted to any 3rd party websites, so if you needed to post a particular not to a customer on eBay or example this would need to be done via eBay messaging or directly via email.