Systems and methods for instrument disturbance compensation include a computer-assisted device. The computer-assisted device includes an articulated arm having a plurality of joints and a control unit coupled to the articulated arm. The control unit is configured to detect a disturbance to the articulated arm caused by a release of one or more brakes of the plurality of joints and maintain a position of a point of interest associated with the articulated arm by compensating for the disturbance using one or more joints of the plurality of joints. In some embodiments, the point of interest is a tip of an end effector of the articulated arm. In some embodiments, the control unit is configured to determine a predicted motion for the point of interest based on the disturbance and send a drive command to move the point of interest in a direction opposite to the predicted motion.