End effector position set point correction includes an instrument having an end effector and a control unit. In some embodiments, the control unit actuates the end effector to a first position, determines an actuation level, determines an offset based on the actuation level, adjusts a position set point based on the offset, and actuates the end effector to the adjusted position set point. In some embodiments, the control unit actuates the end effector, determines an actuation level, and determines whether the actuation level is above a threshold. In response to determining that the actuation level is above the threshold, the control unit determines a position of the end effector, identifies a nominal position associated with the determined position, determines an offset based on the nominal position and the determined position, adjusts a position set point based on the offset, and actuates the end effector to the adjusted position set point.