When trying to ascertain faults on the neg, look at the neg! Not a reproduction.
In repro, whether widgetal or on paper, you have layered potential repro faults to back-track through or mislead.
Quick grab of your sectional; inverted to show what the scanner saw of the negative.
In Red-Circle, is classic dust-mot; completely black 'blocking' light through the film.
In yellow circle... not quite completely white, passing all light through the transparency, something has removed almost all the emulsion. If it was a streak it would more likely be a scratch, small dot like that? not quite completely white, if more common, could be a process error, but its probably not very relevant to the bigger issue. but, on neg, black is added, white taken away, remember. There are other white speckles, that in widgetal could just be the software trying to decide on the colour between it's thresholds! They may not be on the actual negative.
The dark 'speckling' is darker than back-ground, in negative; so is added to, not taken away from; either during dev, as in over dev, or after, as contamination.
Look at Langford's Dark-Room Hand-Book; he provides illustration of lots of common process errors.
And the actual neg.