A medical robotic system includes a control system and a manipulator assembly including actuators to manipulate a flexible elongate body, including a rotation actuator to bend the flexible elongate body. The control system is configured to perform: determining an operational state of the system; detecting a fault in one or more components of the system; classifying the fault with one or more classifications of a plurality of classifications according to heuristics; and imposing a fault reaction state on the system based on the classifications to mitigate the fault. The control system is configured to impose a first fault reaction state for a motion actuation fault and impose a second fault reaction state for a non-motion actuation fault. The first fault reaction state includes controlling the rotation actuator to cause the elongate body to become compliant to external forces placed upon the elongate body by walls of an anatomical passageway.