Thats normally down to your motor missing steps (speed to high, under current, poor driver cooling) or a mehanical fault stopping your axis traveling properly in one direction.
It seems end stops are only good for setting your zero position and not as an emergency stop, as they get ignored whilst jogging axis and only work during homing.
So, if it happens whilst homing you probably have a wiring problem or failing switch, if it happens whilst manually jogging axis its under current or bad driver cooling, belt issues or too much speed..