Clear spots on negatives often arise if there is dust in the camera that falls on to the film at or before the time of exposure. That dust blocks the light from getting to the film. When you print or display a scanned positive from that negative, the spot where the dust is is clear on the negative and black on the print or the screen.
Black specks on the negative re often dirt or dust embedded in the emulsion due to the conditions of either processing or, more commonly, drying.