So, on the negative film there are dark dots surrounded by clearer areas ? Is the surface of the film emulsion smooth where the marks are, or pitted ? It could be mechanical/chemical damage to the film roll before it was chopped up in to 35mm strips, but that is a wild guess. I haven't seen anything precisely like that, and so localised, before.
Edit: I suppose the obvious supplementary questions are what sort of film was used, and how was it processed ?