The OP has identified a key problem with modern film photography: the quality of the labs now left doing the job.
I have tried several, and sometimes it looks like the negatives have been rubbed, emulsion side down, along the floor before cutting them up and putting them in their sleeves. I get exactly the same - odd dust patterns and scratches on the emulsion and water marks and, worse than that, much, much worse, dirty, greasy fingerprints over the neg itself.
If you really like the neg, you can clean up dust using PS, but there is no easy way to remove thumbprints or bad scratches - the neg is simply ruined.
I recently went through the job of scanning in all my thousands of old negs/slides: the interesting thing is that, while many had suffered colour shifts due to age, or had some dust where they had not been in a protective sleeve, NONE of them had thumbprints or scratches. It seems to be an entirely modern phenomenon.
It does make me think about using film, to which I am otherwise dedicated. In reality, I am using specialist labs in the centre of London, England as well, where you would expect consistently good quality. However, it appears not.
I don't want to get into darkroom stuff, don't have the facilities, I have to be able to trust the lab, but at the moment, I can't.
Rant over.
rjstep3