Witness marks are, in their loosest definitions, visual indicators of how (or where) an item should be positioned relative to another item. Many witness marks are made intentionally, like the marks you probably make on a driveshaft to index it correctly when it’s reinstalled. However, in a looser interpretation, a witness mark can also be generated naturally. Often, parts like fasteners and the objects with which they interface generate visual evidence that indicates how the items were positioned or assembled.
That’s sort of a fancy way of saying “tools and fasteners leave marks, which can be used as clues.” For instance, most people working a parts counter have been trained to examine mounting ears on new rotating electrical parts to determine if it’s been installed. If there’s a telltale shiny circle made by a bolt when it was tightened against the part, odds are good that part has been on a car. That circle is a witness mark.