Systems and methods for operating a robotic surgical system are provided. The system includes a surgical tool, a manipulator comprising links for controlling the tool, a navigation system comprising a tracker coupled to the manipulator or the tool and a localizer to monitor a state of the tracker. Controller(s) determine a raw (or lightly filtered) relationship between one or more components of the manipulator and one or more components of the navigation system by utilizing one or more of raw kinematic measurement data from the manipulator and raw navigation data from the navigation system. The controller(s) utilize the raw (or lightly filtered) relationship to determine whether an error has occurred relating to at least one of the manipulator and the navigation system.
