Systems, and methods are provided for computer based method for determining a source of a registration error in a surgical navigation system, by registering at least two patient reference markers in a common coordinate space, positioning at least one reference marker in a known position with respect to at least one of two patient reference markers. A relative position of the at least two patient reference markers with respect to each other in the common coordinate space is monitored, as well as a position of said at least one reference marker with respect to a first of the at least two patient reference markers. Upon detecting a change in relative position of the least at least two patient reference markers with respect to each other, determining if the position of said at least one reference marker with respect to the first of the at least two patient reference markers has changed, and if yes, designating that the first patient reference marker has moved, and if not, designating that the second of the at least two patient reference markers has moved.